gomap-paper-2019.1.def

# Recipe to build the singularity container used to make this paper reproducible
# Instead of building the container yourself, best pull it from https://cloud.sylabs.io/library/merlin/default/gomap-paper-2019.1
Bootstrap: library
From: ubuntu:20.04

%post
  # Add universe repository
  echo "deb http://us.archive.ubuntu.com/ubuntu bionic universe" >> /etc/apt/sources.list
  apt -y update
  # Install utilites
  apt install -y wget vim curl libcurl4-openssl-dev libxml2-dev libssl-dev libpng-dev build-essential
  # Install Crystal
  curl -fsSL https://crystal-lang.org/install.sh | bash
  apt -y install libyaml-dev libgmp-dev libreadline-dev
  # Install Ruby
  apt install -y ruby
  gem install rake
  # Install R
  # update indices
  apt update -qq
  # install two helper packages we need
  apt install -y --no-install-recommends software-properties-common dirmngr
  # add the signing key (by Michael Rutter) for these repos
  # To verify key, run gpg --show-keys /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc 
  # Fingerprint: 298A3A825C0D65DFD57CBB651716619E084DAB9
  wget -qO- https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc | tee -a /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc
  # add the R 4.0 repo from CRAN -- adjust 'focal' to 'groovy' or 'bionic' as needed
  add-apt-repository "deb https://cloud.r-project.org/bin/linux/ubuntu $(lsb_release -cs)-cran40/"
  apt install -y --no-install-recommends r-base
  # Install R libraries (ggplot2, ComplexHeatmap, data.table, circlize, stringr, tools)
  R -e 'install.packages(c("ggplot2", "data.table", "stringr", "tools", "circlize", "BiocManager"))'
  R -e 'BiocManager::install("ComplexHeatmap")'
  # Install PHYLIP
  apt install -y phylip
  # Install newick-utils
  wget http://web.archive.org/web/20190914014444/http://cegg.unige.ch/pub/newick-utils-1.6-Linux-x86_64-disabled-extra.tar.gz
  tar -xzf newick-utils-1.6-Linux-x86_64-disabled-extra.tar.gz
  mv newick-utils-1.6/src/nw_* /usr/local/bin

  
  # Clean
  apt-get clean

%environment
  export LC_ALL="C"

%runscript
  rake

%labels
  Author Thyra