SingularityDef_NoPerlbrew.def

Bootstrap: docker
From: ubuntu:24.04

%labels
  Version 1.6.0
  Author Vladimir Mikryukov, Kessy Abarenkov
  Maintainer vladimir.mikryukov@ut.ee
  Biodiverse 4.99_x
  Perl 5.38.0

%runscript
  exec "$@"

%environment
  export SHELL="/bin/bash"
  export PERL5LIB="/opt/biodiverse/lib"

%post -c /bin/bash

  export DEBIAN_FRONTEND="noninteractive"
  export TZ=UTC

  ## Assign variables with perl path

  ## Assign read and execute access for everyone (+ write access for the owner) to the /opt dir
  chmod -R 755 /opt
  
  ## cpanm default options
  export PERL_CPANM_OPT="--notest --skip-satisfied"
  
  ## Install the required dependencies
  apt update -y \
    && apt install -y software-properties-common \
    && add-apt-repository universe \
    && apt update -y \
    && apt upgrade -y \
    && apt install -y \
      software-properties-common \
      python3 python3-pip \
      zip unzip \
      curl git wget less gawk \
      build-essential ca-certificates \
      cpanminus \
      make cmake libtool automake autoconf pkg-config \
      libffi-dev zlib1g-dev libminizip-dev libexpat1-dev libssl-dev \
      libarmadillo-dev libpoppler-dev liblzma-dev \
      libkml-dev libfreexl-dev libogdi-dev \
      libgdal-dev gdal-bin \
      libgeos-dev librttopo-dev \
      libsqlite3-dev sqlite3 \
      locales language-pack-fi language-pack-en && \
        export LANGUAGE=en_US.UTF-8 && \
        export LANG=en_US.UTF-8 && \
        export LC_ALL=en_US.UTF-8 && \
        locale-gen en_US.UTF-8 && \
        dpkg-reconfigure locales \
    && apt-get autoremove -y \
    && apt-get autoclean -y \
    && rm -rf /var/lib/apt/lists/*
  
  ## Install modules
  cpanm \
    rlib@0.02 \
    ExtUtils::Embed@1.35 \
    Catalyst::Devel@1.42 \
    Module::Compile@0.38 \
    FFI::Build::MM@2.10 \
    FFI::Platypus@2.10 \
    List::Util@1.68 \
    List::MoreUtils@0.430 \
    PDL@2.098 \
    Test2::Harness@1.000155 \
    Text::CSV@2.05 \
    Text::CSV_XS@1.59 \
    Excel::ValueReader::XLSX@1.15 \
    Alien::Build@2.84 \
    Alien::freexl@1.06 \
    Alien::libtiff@1.02 \
    Alien::cmake3@0.08 \
    Alien::sqlite@1.07 \
    Alien::patch@0.15 \
    Alien::patchelf@0.08 \
    FFI::Platypus::Declare@1.34 \
    Alien::geos::af@1.012 \
    Alien::proj@1.30
  
  cpanm \
    Alien::spatialite@1.09 \
    Alien::gdal@1.39

  ## Export LD_LIBRARY_PATH and install Geo::GDAL::FFI
  export LD_LIBRARY_PATH=`perl -MAlien::geos::af -E'print Alien::geos::af->dist_dir . q{/lib}'` \
    && cpanm Geo::GDAL::FFI@0.12
  
  cd /opt
  
  ## Download Biodiverse repo (pull only the latest commit from GitHub)
  ## Latest commit from the master branch (development version)
  git clone --depth 1 https://github.com/shawnlaffan/biodiverse.git
  cd  "biodiverse"
  
  ## Get the updated `cpanfile` with fixed module versions
  wget https://raw.githubusercontent.com/vmikk/biodiverse-docker/main/cpanfile -O cpanfile
  
  ## Install Biodiverse + deps for the current directory
  cpanm --installdeps .
  
  ## Install remaining modules
  cpanm \
    Data::Recursive@1.1.0 \
    Getopt::Long::Descriptive@0.116 \
    List::BinarySearch@0.25 \
    LWP::Protocol::https@6.14 \
    Inline::Module@0.34
  
  ## Install Biodiverse Utils
  cpanm \
    https://github.com/shawnlaffan/biodiverse-utils/releases/download/v1.11/Biodiverse-Utils-1.11.tar.gz
  
%test
  perl -V

  ## Test Biodiverse
  # cd /opt/biodiverse
  # export BD_NO_TEST_GUI=1  #  no need to test the GUI libs load
  # /opt/perl5/perlbrew/perls/perl-5.34.0/bin/prove -l