Dockerfile

# syntax=docker/dockerfile:1

# Comments are provided throughout this file to help you get started.
# If you need more help, visit the Dockerfile reference guide at
# https://docs.docker.com/engine/reference/builder/

ARG PYTHON_VERSION=3.9.18
FROM python:${PYTHON_VERSION}-slim-bullseye as base

# Prevents Python from writing pyc files.
ENV PYTHONDONTWRITEBYTECODE=1

# Keeps Python from buffering stdout and stderr to avoid situations where
# the application crashes without emitting any logs due to buffering.
ENV PYTHONUNBUFFERED=1 \
    PROJECT_DIR=/app

WORKDIR $PROJECT_DIR

# Create a non-privileged user that the app will run under.
# See https://docs.docker.com/develop/develop-images/dockerfile_best-practices/#user
ARG UID=10001
RUN adduser \
    --disabled-password \
    --gecos "" \
    --home "/nonexistent" \
    --shell "/sbin/nologin" \
    --no-create-home \
    --uid "${UID}" \
    appuser

# Install OpenJDK-11 and Python
RUN apt-get update && \
    apt-get install -qy \
    mono-complete \
    openjdk-11-jdk \
    build-essential \
    python-dev && \
    rm -rf /var/lib/apt/lists/* && \
    apt-get -qy autoremove && \
    apt-get clean

# Setup JAVA_HOME -- useful for docker commandline
ENV JAVA_HOME=/usr/lib/jvm/java-11-openjdk-amd64/

# Copy the source code into the container.
COPY setup.py \
     README.md \
     requirements.txt $PROJECT_DIR/
COPY --chown=appuser deTEL $PROJECT_DIR/deTEL
COPY utility $PROJECT_DIR/utility

# Download dependencies as a separate step to take advantage of Docker's caching.
# Leverage a cache mount to /root/.cache/pip to speed up subsequent builds.
# Leverage a bind mount to requirements.txt to avoid having to copy them into
# into this layer.
RUN pip install --no-cache-dir --upgrade pip && \
    pip install --no-cache-dir --upgrade setuptools  && \
    pip install --no-cache-dir --upgrade pip-tools && \
    pip install https://extras.wxpython.org/wxPython4/extras/linux/gtk3/debian-11/wxPython-4.2.1-cp39-cp39-linux_x86_64.whl && \
    pip install .

COPY --chown=appuser binaries/fragpipe_v21_1 /fragpipe
ENV PATH="$PATH:/fragpipe/bin"

RUN mkdir -m 777 $PROJECT_DIR/inputs

# Switch to the non-privileged user to run the application.
USER appuser

# Run the application.
ENTRYPOINT ["python", "-m", "deTEL", "rTEL"]
CMD []