rnapdbee-adapters/Dockerfile at main · rnapdbee/rnapdbee-adapters · GitHub

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FROM python:3.13-bookworm AS builder

RUN apt-get update \
 && apt-get install --no-install-recommends -y \
      bison \
      cmake \
      flex \
 && rm -rf /var/lib/apt/lists/*

COPY requirements.txt .

RUN python -m venv /opt/venv \
 && . /opt/venv/bin/activate \
 && pip install --upgrade pip \
 && pip install --no-cache-dir -r requirements.txt

#######################################

FROM python:3.13-slim-bookworm

ENV PYTHONUNBUFFERED=1 \
    PYTHONDONTWRITEBYTECODE=1 \
    PYTHONPATH=/rnapdbee-adapters/src

RUN apt-get update -y \
 && apt-get install -y \
       ca-certificates \
       dirmngr \
       gnupg \
 && rm -rf /var/lib/apt/lists/*

# Install Mono
RUN gpg --homedir /tmp --no-default-keyring --keyring gnupg-ring:/usr/share/keyrings/mono-official-archive-keyring.gpg --keyserver hkp://keyserver.ubuntu.com:80 --recv-keys 3FA7E0328081BFF6A14DA29AA6A19B38D3D831EF \
 && chmod +r /usr/share/keyrings/mono-official-archive-keyring.gpg \
 && echo "deb [signed-by=/usr/share/keyrings/mono-official-archive-keyring.gpg] https://download.mono-project.com/repo/debian stable-buster main" | tee /etc/apt/sources.list.d/mono-official-stable.list \
 && apt-get update \
 && apt-get install -y --no-install-recommends \
      mono-devel \
 && rm -rf /var/lib/apt/lists/*

# Install HiGHS (https://github.com/JuliaBinaryWrappers/HiGHSstatic_jll.jl/releases/download/HiGHSstatic-v1.11.0%2B1/HiGHSstatic.v1.11.0.x86_64-linux-gnu-cxx11.tar.gz)
ADD app/HiGHSstatic.v1.11.0.x86_64-linux-gnu-cxx11.tar.gz /usr/local

# Install svgcleaner (https://github.com/RazrFalcon/svgcleaner/releases/download/v0.9.5/svgcleaner_linux_x86_64_0.9.5.tar.gz)
ADD app/svgcleaner_linux_x86_64_0.9.5.tar.gz /usr/local/bin

# Install IronPython (https://github.com/IronLanguages/ironpython3/releases/download/v3.4.2/ironpython_3.4.2.deb)
COPY app/ironpython_3.4.2.deb /tmp/ironpython_3.4.2.deb
RUN dpkg -i /tmp/ironpython_3.4.2.deb

# PseudoViewer wrapper
COPY app/pseudoviewer/ /pseudoviewer/

ENV PATH="/opt/venv/bin:/pseudoviewer:${PATH}" \
    VIRTUAL_ENV="/opt/venv" \
    ADAPTERS_GUNICORN_LOG_LEVEL=INFO \
    ADAPTERS_MAX_REQUESTS=10 \
    ADAPTERS_PSEUDOVIEWER_TIMEOUT=60 \
    ADAPTERS_RNAPUZZLER_LOG_JSON=false \
    ADAPTERS_THREADS=1 \
    ADAPTERS_WORKERS=4 \
    ADAPTERS_WORKER_TIMEOUT=1200 \
    CLI2REST_BARNABA_URL=http://localhost:8000 \
    CLI2REST_BPNET_URL=http://localhost:8000 \
    CLI2REST_FR3D_URL=http://localhost:8000 \
    CLI2REST_MAXIT_URL=http://localhost:8000 \
    CLI2REST_MCANNOTATE_URL=http://localhost:8000 \
    CLI2REST_RCHIE_URL=http://localhost:8000 \
    CLI2REST_RNAVIEW_URL=http://localhost:8000 \
    CLI2REST_RNAPUZZLER_URL=http://localhost:8000

EXPOSE 80

COPY docker-entrypoint.sh /
RUN chmod +x /docker-entrypoint.sh
ENTRYPOINT ["/docker-entrypoint.sh"]

COPY --from=builder /opt/venv /opt/venv

COPY src/adapters /rnapdbee-adapters/src/adapters