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author galaxytrakr
date Tue, 15 Sep 2026 12:02:36 +0000
parents dd206296acbf
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1 # =============================================================
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2 # Dockerfile for mitokmer2 (compatible with Galaxy/AWS Batch)
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3 # =============================================================
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4
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5 # ---------- Build Stage ----------
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6 FROM ubuntu:focal AS build
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7
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8 ARG DEBIAN_FRONTEND=noninteractive
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9 ARG PYTHON_VER="3.8"
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11 WORKDIR /workspace
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14 # Build dependencies: compiler, zlib dev headers, git, Python
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15 RUN apt-get update && apt-get install -y --no-install-recommends \
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16 build-essential \
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17 g++ \
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18 git \
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19 wget \
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20 zlib1g-dev \
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21 ca-certificates \
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22 python${PYTHON_VER} \
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23 python${PYTHON_VER}-dev \
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24 python${PYTHON_VER}-venv \
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25 && rm -rf /var/lib/apt/lists/*
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26
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27 # Create Python virtual environment using --copies so symlinks
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28 # do not break when the venv is copied to the runtime stage
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29 RUN python${PYTHON_VER} -m venv --copies /opt/venv
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30 ENV PATH="/opt/venv/bin:${PATH}"
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31
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32 # Install Python dependencies
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33 RUN pip install --no-cache-dir -U pip && \
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34 pip install --no-cache-dir pandas
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35
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36 # Clone mitokmer2 source code from GitHub
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37 RUN git clone https://github.com/mmammel8/mitokmer2.git /opt/mitokmer2
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38
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39 WORKDIR /opt/mitokmer2
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40
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41 # Compile kmer_read_1.cpp -> kmerread7
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42 # kmer_read_m7.py calls ./kmerread7 as a subprocess
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43 RUN g++ -O3 kmer_read_1.cpp -o kmerread7 -lz && \
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44 chmod +x kmerread7
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46 # Install any Python requirements declared in the repo
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47 RUN if [ -f requirements.txt ]; then \
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48 pip install --no-cache-dir -r requirements.txt; \
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49 fi
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51
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52 # ---------- Runtime Stage ----------
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53 FROM ubuntu:focal AS runtime
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54
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55 ARG DEBIAN_FRONTEND=noninteractive
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56
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57 # Lean runtime: zlib shared library + Python runtime only
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58 RUN apt-get update && apt-get install -y --no-install-recommends \
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59 zlib1g \
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60 libbz2-1.0 \
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61 ca-certificates \
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62 python3.8 \
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63 python3.8-venv \
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64 python3.8-distutils \
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65 && rm -rf /var/lib/apt/lists/*
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66
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67 # Copy compiled binary from build stage
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68 # kmerread7 is called by kmer_read_m7.py as ./kmerread7 so it
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69 # must be in the working directory at runtime; place it in both
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70 # /usr/local/bin (for PATH) and /opt/mitokmer2 (for relative invocation)
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71 COPY --from=build /opt/mitokmer2/kmerread7 /usr/local/bin/kmerread7
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72 COPY --from=build /opt/mitokmer2/kmerread7 /opt/mitokmer2/kmerread7
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73
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74 # Copy Python scripts and supporting files from build stage
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75 COPY --from=build /opt/mitokmer2 /opt/mitokmer2
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76
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77 # Copy Python virtual environment from build stage
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78 COPY --from=build /opt/venv /opt/venv
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79
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80 # Refresh the dynamic linker cache
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81 RUN ldconfig || true
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82
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83 # Ensure all users (including arbitrary Galaxy UIDs) can
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84 # read and execute binaries, scripts, and the venv
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85 RUN chmod a+rx /usr/local/bin/kmerread7 \
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86 /opt/mitokmer2/kmerread7 && \
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87 chmod -R a+rX /opt/mitokmer2 && \
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88 chmod -R a+rX /opt/venv
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89
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90 # Runtime environment
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91 ENV PATH="/opt/venv/bin:/opt/mitokmer2:/usr/local/bin:${PATH}" \
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92 LC_ALL=C
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93
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94 # IMPORTANT: No ENTRYPOINT for Galaxy/AWS Batch. Neutral CMD.
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95 CMD ["/bin/bash"]