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author galaxytrakr
date Mon, 14 Sep 2026 20:27:08 +0000
parents dd206296acbf
children ecf96ad08611
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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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10
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11 WORKDIR /workspace
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12
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13 # Build dependencies: compiler, zlib dev headers, git, Python
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14 RUN apt-get update && apt-get install -y --no-install-recommends \
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15 build-essential \
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16 g++ \
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17 git \
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18 wget \
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19 zlib1g-dev \
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20 ca-certificates \
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21 python${PYTHON_VER} \
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22 python${PYTHON_VER}-dev \
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23 python${PYTHON_VER}-venv \
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24 && rm -rf /var/lib/apt/lists/*
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25
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26 # Create Python virtual environment using --copies so symlinks
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27 # do not break when the venv is copied to the runtime stage
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28 RUN python${PYTHON_VER} -m venv --copies /opt/venv
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29 ENV PATH="/opt/venv/bin:${PATH}"
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30
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31 # Install Python dependencies
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32 RUN pip install --no-cache-dir -U pip && \
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33 pip install --no-cache-dir pandas
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34
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35 # Clone mitokmer2 source code from GitHub
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36 RUN git clone https://github.com/mmammel8/mitokmer2.git /opt/mitokmer2
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37
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38 WORKDIR /opt/mitokmer2
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39
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40 # Compile kmer_read_1.cpp -> kmerread7
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41 # kmer_read_m7.py calls ./kmerread7 as a subprocess
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42 RUN g++ -O3 kmer_read_1.cpp -o kmerread7 -lz && \
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43 chmod +x kmerread7
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44
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45 # Install any Python requirements declared in the repo
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46 RUN if [ -f requirements.txt ]; then \
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47 pip install --no-cache-dir -r requirements.txt; \
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48 fi
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50
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51 # ---------- Runtime Stage ----------
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52 FROM ubuntu:focal AS runtime
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53
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54 ARG DEBIAN_FRONTEND=noninteractive
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55
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56 # Lean runtime: zlib shared library + Python runtime only
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57 RUN apt-get update && apt-get install -y --no-install-recommends \
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58 zlib1g \
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59 libbz2-1.0 \
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60 ca-certificates \
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61 python3.8 \
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62 python3.8-venv \
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63 python3.8-distutils \
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64 && rm -rf /var/lib/apt/lists/*
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65
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66 # Copy compiled binary from build stage
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67 # kmerread7 is called by kmer_read_m7.py as ./kmerread7 so it
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68 # must be in the working directory at runtime; place it in both
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69 # /usr/local/bin (for PATH) and /opt/mitokmer2 (for relative invocation)
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70 COPY --from=build /opt/mitokmer2/kmerread7 /usr/local/bin/kmerread7
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71 COPY --from=build /opt/mitokmer2/kmerread7 /opt/mitokmer2/kmerread7
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72
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73 # Copy Python scripts and supporting files from build stage
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74 COPY --from=build /opt/mitokmer2 /opt/mitokmer2
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75
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76 # Copy Python virtual environment from build stage
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77 COPY --from=build /opt/venv /opt/venv
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78
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79 # Refresh the dynamic linker cache
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80 RUN ldconfig || true
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81
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82 # Ensure all users (including arbitrary Galaxy UIDs) can
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83 # read and execute binaries, scripts, and the venv
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84 RUN chmod a+rx /usr/local/bin/kmerread7 \
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85 /opt/mitokmer2/kmerread7 && \
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86 chmod -R a+rX /opt/mitokmer2 && \
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87 chmod -R a+rX /opt/venv
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88
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89 # Runtime environment
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90 ENV PATH="/opt/venv/bin:/opt/mitokmer2:/usr/local/bin:${PATH}" \
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91 LC_ALL=C
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92
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93 # IMPORTANT: No ENTRYPOINT for Galaxy/AWS Batch. Neutral CMD.
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94 CMD ["/bin/bash"]