Singularity.0.4.0

Bootstrap: docker
From: nvcr.io/nvidia/cuda:10.2-devel-ubuntu18.04

%labels
Maintainer marty.hickman@plantandfood.co.nz
Version 0.4.0

%post
  ## Download build prerequisites
  apt-get update
  apt-get -y install python3-pip zlib1g-dev
  ## Install
  pip3 install ont-bonito==0.4.0 || true
  rm -rf /root/.cache

%runscript
if [ ! -f /usr/local/lib/python3.6/dist-packages/bonito/models/dna_r9.4.1.hdf5 ]; then
  exec /bin/echo -e "This container requires that you bind mount the location of Bonito pre-trained models data into `/usr/local/lib/python3.6/dist-packages/bonito/models/`. Please use \"singularity run -B <path_to_bonito_models>:/usr/local/lib/python3.6/dist-packages/bonito/models $SINGULARITY_NAME\" and try again. You can download the pre-trained models with \"bonito download\". See https://github.com/nanoporetech/bonito#models for more information."
else
  exec bonito "$@"
fi