Mercurial > repos > galaxytrakr > mitokmer

comparison Dockerfile @ 2:dd206296acbf draft

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planemo upload commit 83cba09882dc583100b39b69b41cf791e4efb55a
author galaxytrakr
date Mon, 14 Sep 2026 19:47:05 +0000
parents adc887a1a6de
children ecf96ad08611
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1:e6b5e7a0d7e7 2:dd206296acbf
35 # Clone mitokmer2 source code from GitHub 35 # Clone mitokmer2 source code from GitHub
36 RUN git clone https://github.com/mmammel8/mitokmer2.git /opt/mitokmer2 36 RUN git clone https://github.com/mmammel8/mitokmer2.git /opt/mitokmer2
37 37
38 WORKDIR /opt/mitokmer2 38 WORKDIR /opt/mitokmer2
39 39
40 # Compile the C++ read-screening program 40 # Compile kmer_read_1.cpp -> kmerread7
41 # kmer_read_1.cpp -> kmerread 41 # kmer_read_m7.py calls ./kmerread7 as a subprocess
42 RUN g++ -O3 kmer_read_1.cpp -o kmerread -lz && \ 42 RUN g++ -O3 kmer_read_1.cpp -o kmerread7 -lz && \
43 chmod +x kmerread 43 chmod +x kmerread7
44 44
45 # Install any Python requirements declared in the repo 45 # Install any Python requirements declared in the repo
46 RUN if [ -f requirements.txt ]; then \ 46 RUN if [ -f requirements.txt ]; then \
47 pip install --no-cache-dir -r requirements.txt; \ 47 pip install --no-cache-dir -r requirements.txt; \
48 fi 48 fi
62 python3.8-venv \ 62 python3.8-venv \
63 python3.8-distutils \ 63 python3.8-distutils \
64 && rm -rf /var/lib/apt/lists/* 64 && rm -rf /var/lib/apt/lists/*
65 65
66 # Copy compiled binary from build stage 66 # Copy compiled binary from build stage
67 COPY --from=build /opt/mitokmer2/kmerread /usr/local/bin/kmerread 67 # kmerread7 is called by kmer_read_m7.py as ./kmerread7 so it
68 # must be in the working directory at runtime; place it in both
69 # /usr/local/bin (for PATH) and /opt/mitokmer2 (for relative invocation)
70 COPY --from=build /opt/mitokmer2/kmerread7 /usr/local/bin/kmerread7
71 COPY --from=build /opt/mitokmer2/kmerread7 /opt/mitokmer2/kmerread7
68 72
69 # Copy Python scripts and supporting files from build stage 73 # Copy Python scripts and supporting files from build stage
70 COPY --from=build /opt/mitokmer2 /opt/mitokmer2 74 COPY --from=build /opt/mitokmer2 /opt/mitokmer2
71 75
72 # Copy Python virtual environment from build stage 76 # 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 77 COPY --from=build /opt/venv /opt/venv
75 78
76 # Refresh the dynamic linker cache so zlib and other shared 79 # Refresh the dynamic linker cache
77 # libraries are found at runtime
78 RUN ldconfig || true 80 RUN ldconfig || true
79 81
80 # Ensure all users (including arbitrary Galaxy UIDs) can 82 # Ensure all users (including arbitrary Galaxy UIDs) can
81 # read and execute binaries, scripts, and the venv 83 # read and execute binaries, scripts, and the venv
82 RUN chmod a+rx /usr/local/bin/kmerread && \ 84 RUN chmod a+rx /usr/local/bin/kmerread7 \
85 /opt/mitokmer2/kmerread7 && \
83 chmod -R a+rX /opt/mitokmer2 && \ 86 chmod -R a+rX /opt/mitokmer2 && \
84 chmod -R a+rX /opt/venv 87 chmod -R a+rX /opt/venv
85 88
86 # Runtime environment 89 # Runtime environment
87 ENV PATH="/opt/venv/bin:/opt/mitokmer2:/usr/local/bin:${PATH}" \ 90 ENV PATH="/opt/venv/bin:/opt/mitokmer2:/usr/local/bin:${PATH}" \