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comparison Dockerfile @ 0:adc887a1a6de draft

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planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
author galaxytrakr
date Fri, 11 Sep 2026 21:58:43 +0000
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-1:000000000000 0:adc887a1a6de
1 # =============================================================
2 # Dockerfile for mitokmer2 (compatible with Galaxy/AWS Batch)
3 # =============================================================
4
5 # ---------- Build Stage ----------
6 FROM ubuntu:focal AS build
7
8 ARG DEBIAN_FRONTEND=noninteractive
9 ARG PYTHON_VER="3.8"
10
11 WORKDIR /workspace
12
13 # Build dependencies: compiler, zlib dev headers, git, Python
14 RUN apt-get update && apt-get install -y --no-install-recommends \
15 build-essential \
16 g++ \
17 git \
18 wget \
19 zlib1g-dev \
20 ca-certificates \
21 python${PYTHON_VER} \
22 python${PYTHON_VER}-dev \
23 python${PYTHON_VER}-venv \
24 && rm -rf /var/lib/apt/lists/*
25
26 # Create Python virtual environment using --copies so symlinks
27 # do not break when the venv is copied to the runtime stage
28 RUN python${PYTHON_VER} -m venv --copies /opt/venv
29 ENV PATH="/opt/venv/bin:${PATH}"
30
31 # Install Python dependencies
32 RUN pip install --no-cache-dir -U pip && \
33 pip install --no-cache-dir pandas
34
35 # Clone mitokmer2 source code from GitHub
36 RUN git clone https://github.com/mmammel8/mitokmer2.git /opt/mitokmer2
37
38 WORKDIR /opt/mitokmer2
39
40 # Compile the C++ read-screening program
41 # kmer_read_1.cpp -> kmerread
42 RUN g++ -O3 kmer_read_1.cpp -o kmerread -lz && \
43 chmod +x kmerread
44
45 # Install any Python requirements declared in the repo
46 RUN if [ -f requirements.txt ]; then \
47 pip install --no-cache-dir -r requirements.txt; \
48 fi
49
50
51 # ---------- Runtime Stage ----------
52 FROM ubuntu:focal AS runtime
53
54 ARG DEBIAN_FRONTEND=noninteractive
55
56 # Lean runtime: zlib shared library + Python runtime only
57 RUN apt-get update && apt-get install -y --no-install-recommends \
58 zlib1g \
59 libbz2-1.0 \
60 ca-certificates \
61 python3.8 \
62 python3.8-venv \
63 python3.8-distutils \
64 && rm -rf /var/lib/apt/lists/*
65
66 # Copy compiled binary from build stage
67 COPY --from=build /opt/mitokmer2/kmerread /usr/local/bin/kmerread
68
69 # Copy Python scripts and supporting files from build stage
70 COPY --from=build /opt/mitokmer2 /opt/mitokmer2
71
72 # Copy Python virtual environment from build stage
73 # --copies in the build stage ensures no broken symlinks here
74 COPY --from=build /opt/venv /opt/venv
75
76 # Refresh the dynamic linker cache so zlib and other shared
77 # libraries are found at runtime
78 RUN ldconfig || true
79
80 # Ensure all users (including arbitrary Galaxy UIDs) can
81 # read and execute binaries, scripts, and the venv
82 RUN chmod a+rx /usr/local/bin/kmerread && \
83 chmod -R a+rX /opt/mitokmer2 && \
84 chmod -R a+rX /opt/venv
85
86 # Runtime environment
87 ENV PATH="/opt/venv/bin:/opt/mitokmer2:/usr/local/bin:${PATH}" \
88 LC_ALL=C
89
90 # IMPORTANT: No ENTRYPOINT for Galaxy/AWS Batch. Neutral CMD.
91 CMD ["/bin/bash"]