SharedPolymorphismsDaphnia/Apptainer.def at main · connor122721/SharedPolymorphismsDaphnia · GitHub

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Bootstrap: docker
From: rocker/r-ver:4.3.1

%post
    apt-get update && apt-get install -y \
        libcurl4-openssl-dev \
        libssl-dev \
        libxml2-dev \
        libgdal-dev \
        libgeos-dev \
        libproj-dev \
        python3 \
        python3-pip

    R -e "install.packages(c('data.table', 'foreach', 'tidyverse', 'ggforce', 'viridis', 'cowplot', 'phylobase', 'ggtree', 'colortools', 'phylotools', 'phytools', 'thacklr', 'treespace', 'TreeTools'), repos='http://cran.rstudio.com/')"
    R -e "install.packages('BiocManager', repos='http://cran.rstudio.com/')"
    R -e "BiocManager::install(c('SeqArray', 'doParallel', 'SNPRelate'))"

    pip3 install numpy pandas matplotlib seaborn scikit-learn moments-popgen

%environment
    export PATH=/usr/local/bin:$PATH

%labels
    Author "Connor S. Murray"
    Version "1.0"

%help
    This is an Apptainer definition file for creating a container with the necessary R and Python packages for running scripts in the SharedPolymorphismsDaphnia repository.

%runscript
    exec R