Singularity.180922

Bootstrap: docker
From: ubuntu:bionic

%labels
Maintainer ben.warren@plantandfood.co.nz
Version 180922

%environment
  PATH=/opt/3d-dna:$PATH
  export PATH

%post
  ## Download build prerequisites
  export DEBIAN_FRONTEND=noninteractive
  export TZ="Pacific/Auckland"
  apt-get update
  apt-get -y install git make openjdk-8-jre parallel python-matplotlib python-numpy python-scipy wget
  
  ## Install LastZ (version 1.03.73 released 20150708)
  wget http://www.bx.psu.edu/~rsharris/lastz/newer/lastz-1.03.73.tar.gz
  tar -xzf lastz-1.03.73.tar.gz
  cd lastz-distrib-1.03.73/src
  sed -i 's/-Werror //' Makefile
  make
  LASTZ_INSTALL=/usr/bin/ make install

  ## Install 3d-dna
  cd /opt
  git clone https://github.com/theaidenlab/3d-dna.git
  cd 3d-dna
  git checkout 3f18163
  chmod +x run-asm-pipeline.sh run-asm-pipeline-post-review.sh

  ## Cleanup
  apt-get -y remove git make wget
  apt-get -y clean all
  rm -rf /lastz*

%runscript
if [ -x /opt/3d-dna/$SINGULARITY_NAME ]; then
    exec $SINGULARITY_NAME "$@"
else
    /bin/echo -e "This Singularity image cannot provide a single entrypoint. Please use \"singularity exec $SINGULARITY_NAME <cmd>\", where <cmd> is one of the following:\n"
    exec find /opt/3d-dna -maxdepth 1 -type f -executable -printf '%f\n'
fi