Apptainer.4.1.0

Bootstrap: docker
From: ubuntu:jammy

%labels
Maintainer marty.hickman@plantandfood.co.nz
Version 4.1.0

%environment
  PATH=/opt/MaSuRCA-4.1.0/bin:$PATH
  export PATH
  export LANG=en_NZ.UTF-8
  export LC_ALL=en_NZ.UTF-8
  export LANGUAGE=en_NZ.UTF-8

%post
  ## Download build prerequisites
  apt-get update && apt-get install -y \
    curl build-essential libboost-dev libbz2-dev wget zlib1g-dev locales libenv-path-perl
  locale-gen en_NZ.UTF-8


  ## Build
  cd /opt
  curl -s -L https://github.com/alekseyzimin/masurca/releases/download/v4.1.0/MaSuRCA-4.1.0.tar.gz | tar xz
  cd MaSuRCA-4.1.0
  # Fix the install script from exiting with a copy error
  sed -i 's/cp -a ..\/Flye /cd /' install.sh
  ./install.sh

  ## Do some cleanup
  apt-get -y remove --purge build-essential
  apt-get -y clean all 
  apt-get -y autoremove --purge

%runscript
 if [ -x /opt/MaSuRCA-4.1.0/bin/$APPTAINER_NAME ]; then
    exec $APPTAINER_NAME "$@"
 else
    /bin/echo -e "This Apptainer image cannot provide a single entrypoint. Please use \"apptainer exec $APPTAINER_NAME <cmd>\", where <cmd> is one of the following:\n"
    exec ls /opt/MaSuRCA-4.1.0/bin
 fi