singularity-geospatial-r/Singularity.latest at main · AdamWilsonLab/singularity-geospatial-r · GitHub

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Bootstrap: docker
From: rocker/geospatial

%labels
  Author Adam M. Wilson
  Version 0.0.1

%apprun rserver
    exec rserver "${@}"

%runscript
    exec rserver "${@}"

%startscript
    echo "Container was created $NOW"
    echo "RUNNING rserver startscript"
    echo "Arguments received: $*"
    echo user = $USER      password = $PASSWORD     port = $PORT
    rserver  "$@"

%post

  # Add some linux libraries (needed for R packages or otherwise)
  apt-get update -y
  apt-get upgrade -y  --allow-unauthenticated
  apt-get install -y --no-install-recommends --allow-unauthenticated \
        locales \
        libssl-dev \
        libxml2-dev \
        libcairo2-dev \
        libxt-dev \
        libcgal-dev \
        libglu1-mesa-dev \
        ca-certificates \
        netcat\
        libsecret-1-0 \
        jags

        NOW=`date`
        echo "export NOW=\"${NOW}\"" >> $SINGULARITY_ENVIRONMENT

  # Add a default CRAN mirror
  mkdir -p /usr/lib/R/etc/
  echo "options(repos = c(CRAN = 'https://cran.rstudio.com/'), download.file.method = 'libcurl')" >> /usr/lib/R/etc/Rprofile.site

  # Add a directory for host R libraries
  mkdir -p /library
  echo "R_LIBS_SITE=/library:\${R_LIBS_SITE}" >> /usr/lib/R/etc/Renviron.site

  # install some extra R packages
  R -e "install.packages('maxnet', method='wget', quiet=T, verbose=F)"
  R -e "install.packages('Morpho', method='wget', quiet=T, verbose=F)"
  R -e "install.packages('rgl', method='wget', quiet=T, verbose=F)"
  R -e "install.packages('ENMeval', method='wget', quiet=T, verbose=F)"
  R -e "install.packages('scales', method='wget', quiet=T, verbose=F)"
  R -e "install.packages('viridis', method='wget', quiet=T, verbose=F)"
  R -e "install.packages('rjags', method='wget', quiet=T, verbose=F)"
  R -e "install.packages('coda', method='wget', quiet=T, verbose=F)"
  R -e "install.packages('mcmc', method='wget', quiet=T, verbose=F)"
  R -e "install.packages('colourvalues', method='wget', quiet=T, verbose=F)"
  R -e "install.packages('BiocManager', method='wget', quiet=T, verbose=F)"
  R -e "install.packages('keyring', method='wget', quiet=T, verbose=F)"
  R -e "install.packages('ENMTools', method='wget', quiet=T, verbose=F)"
  R -e "BiocManager::install('rhdf5')"