rxp-pipeline-singularity.def

Bootstrap: docker
From: ubuntu:20.04

%setup
    # Copy LiDAR plugin and wrapper script
    cp -r /data/requests/peer_rev/21_27_wilkes_tls_classification/code/rivlib-2_5_10-x86_64-linux-gcc9 /tmp/
    # Copy code
    mkdir -p /tmp/code && cp -a . /tmp/code

%post
    # Set as non-interactve
    export DEBIAN_FRONTEND=noninteractive

    # Install some standard packages, including compilers
    apt-get update && apt-get install -y  \
        apt-utils git curl vim unzip wget \
        build-essential


    # Install miniconda
    wget --quiet https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O ~/miniconda.sh && \
        /bin/bash ~/miniconda.sh -b -p /opt/miniconda && \
        rm ~/miniconda.sh && \
        ln -s /opt/miniconda/etc/profile.d/conda.sh /etc/profile.d/conda.sh && \

    . /opt/miniconda/etc/profile.d/conda.sh
    conda activate base
    # Create environment
    conda create -n pdal -c conda-forge gdal ninja cmake cxx-compiler laszip pdal python-pdal pandas tqdm

    conda activate pdal

    # Build PDAL with plugin
    wget https://github.com/PDAL/PDAL/releases/download/2.3.0/PDAL-2.3.0-src.tar.gz
    tar xf PDAL-2.3.0-src.tar.gz
    cd PDAL-2.3.0-src/
    sed -i 's/DEFAULT_SYNC_TO_PPS = true/DEFAULT_SYNC_TO_PPS = false/g' plugins/rxp/io/RxpReader.hpp
    export RiVLib_DIR=/tmp/rivlib-2_5_10-x86_64-linux-gcc9
    mkdir build
    cd build
    cmake -G Ninja -D BUILD_PLUGIN_RIVLIB=ON -D CMAKE_INSTALL_PREFIX=/opt/miniconda/envs/pdal ../
    ninja
    ninja install
    conda clean --all -y

    mv /tmp/code /code/

%runscript
	# Call wrapper script to run pipeline.
    export PATH=/opt/miniconda/envs/pdal/bin:$PATH
    /code/run_rxp.sh $1

%labels
    Author neodaas-ai@pml.ac.uk

%help
    Container to run the initial data preprocessing for TLS processing