SpaMTP/spamtp.def at main · GenomicsMachineLearning/SpaMTP · GitHub

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Bootstrap: docker
From: condaforge/mambaforge:latest

%files
    environment-linux.yml /opt/environment-linux.yml
    dependencies.R /opt/dependencies.R

%environment
    export PATH=/opt/conda/bin:$PATH
    export LD_LIBRARY_PATH=/opt/conda/lib:$LD_LIBRARY_PATH

%post -c /bin/bash
    set -e

    # Configure tzdata noninteractively
    export DEBIAN_FRONTEND=noninteractive
    export TZ=Etc/UTC
    ln -snf /usr/share/zoneinfo/$TZ /etc/localtime && echo $TZ > /etc/timezone

    # System packages
    apt-get update && apt-get install -y \
        build-essential \
        wget \
        git \
        openjdk-11-jdk \
        libfontconfig1 \
        libharfbuzz-dev \
        libfribidi-dev \
        libfreetype6-dev \
        libpng-dev \
        libtiff5-dev \
        libjpeg-dev \
        libxml2-dev \
        libcairo2-dev

    # Set up conda environment
    . /opt/conda/etc/profile.d/conda.sh
    conda config --set solver libmamba

    # Create conda environment from yml
    conda env create --prefix /opt/conda/envs/spamtp --file=/opt/environment-linux.yml -y
    conda activate /opt/conda/envs/spamtp

    # Install R dependencies
    Rscript /opt/dependencies.R

    # Clean up
    conda clean -afy
    apt-get clean
    rm -rf /var/lib/apt/lists/*

%runscript
   echo "Container for spamtp environment"
    echo "Activate the conda environment with: conda activate /opt/conda/envs/spamtp"
    exec "$@"

%labels
    Author andrew.newman@uq.edu.au
    Version v1.0
    Description spamtp analysis environment container