moma-preprocessing/Dockerfile at master · nimwegenLab/moma-preprocessing · GitHub

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FROM continuumio/miniconda3:22.11.1 as python_script_builder
# build container for building stand-alone executable of moma_preprocess

RUN apt-get update && \
    apt-get install -y binutils

WORKDIR /build_dir

# REFs:
# https://anaconda.org/conda-forge/pyinstaller
RUN conda create -y -n moma-preprocess python=3.10 pyinstaller=5.6

WORKDIR /build_dir/moma_preprocess
# Use `conda run`, because `conda activate` fails in containers; see here: https://pythonspeed.com/articles/activate-conda-dockerfile/#working
SHELL ["conda", "run", "--no-capture-output", "-n", "moma-preprocess", "/bin/bash", "-c"]

# Build stand-alone `moma_preprocess` executable of `moma_preprocess` Python script
# Output path is: /build_dir/moma/dist/moma_preprocess
WORKDIR /build_dir/moma_preprocess
COPY docker/moma_preprocess moma_preprocess
RUN pyinstaller --onefile --name moma_preprocess moma_preprocess


FROM continuumio/miniconda3:22.11.1

ARG build_dir="/build_dir"
ARG exec_dir="/preprocessing"

RUN apt-get update && apt-get install -y ffmpeg libsm6 libxext6

RUN mkdir -p $build_dir

# setup conda environment
COPY conda/conda_package_list.txt $build_dir/conda_package_list.txt
COPY conda/conda_environment_setup.sh $build_dir/conda_environment_setup.sh
RUN chmod +x $build_dir/conda_environment_setup.sh
RUN $build_dir/conda_environment_setup.sh

# setup mmpreprocesspy package
COPY mmpreprocesspy $build_dir/mmpreprocesspy
COPY conda/conda_package_setup.sh $build_dir/conda_package_setup.sh
RUN chmod +x $build_dir/conda_package_setup.sh
RUN $build_dir/conda_package_setup.sh

COPY call_preproc_fun.py $exec_dir/call_preproc_fun.py
COPY docker/call_preproc_fun.sh $exec_dir/call_preproc_fun.sh
RUN chmod +x $exec_dir/call_preproc_fun.sh

ARG host_scripts="/host_scripts"
RUN mkdir $host_scripts
COPY docker/mm_dispatch_preprocessing.sh $host_scripts/mm_dispatch_preprocessing.sh
COPY --from=python_script_builder /build_dir/moma_preprocess/dist/moma_preprocess $host_scripts/moma_preprocess


ENTRYPOINT ["/preprocessing/call_preproc_fun.sh"]