Dockerfile_input

# Start from python image
FROM python:3.12 AS stage0

# Set working directory
WORKDIR /app

# Install Python build dependencies and Python libraries
RUN apt-get update && apt-get install -y --no-install-recommends \
    build-essential \
    git \
    curl \
    && rm -rf /var/lib/apt/lists/*

COPY requirements.txt .
RUN pip install --upgrade pip setuptools \
    && pip install -r requirements.txt \
    && pip install zarr==2.18.2

# Install system libraries for R and geospatial packages
RUN apt-get update && apt-get install -y --no-install-recommends \
    build-essential \
    libgdal-dev \
    gdal-bin \
    libgeos-dev \
    libproj-dev \
    default-libmysqlclient-dev \
    libudunits2-dev \
    libssl-dev \
    libxml2-dev \
    libcurl4-openssl-dev \
    cmake \
    libprotobuf-dev \
    protobuf-compiler \
    locales \
    && echo "en_US.UTF-8 UTF-8" >> /etc/locale.gen \
    && locale-gen \
    && rm -rf /var/lib/apt/lists/*

ENV LANG=en_US.UTF-8 \
    LC_ALL=en_US.UTF-8

# Add docker user and set up R library folder
RUN useradd -s /bin/bash -m docker \
    && usermod -a -G staff docker \
    && mkdir -p /usr/local/lib/R/site-library \
    && chown root:staff /usr/local/lib/R/site-library \
    && chmod g+ws /usr/local/lib/R/site-library

# Install R and basic R packages
RUN apt-get update && apt-get install -y --no-install-recommends \
    littler \
    r-base \
    r-base-dev \
    r-recommended \
    r-cran-docopt \
    && rm -rf /var/lib/apt/lists/*

# Install R package dependencies
COPY requirements.R .
RUN Rscript requirements.R

FROM stage0 AS stage1
#move all the scripts needed
COPY /src/lakeflow_1.R .
RUN mkdir ./src
COPY /src/geoglows_aws_pull.py ./src

LABEL version="1.0" \
      description="Containerized lakeflow module." \
      "algorithm.contact"="??"

ENTRYPOINT [ "/usr/bin/Rscript", "/app/lakeflow_1.R" ]