DNAscent.def

Bootstrap: docker
From: nvidia/cuda:11.0.3-cudnn8-devel-ubuntu20.04

%labels
    Version v4.0.3

%help
    DNAscent is software for detecting regions of BrdU and EdU incorporation in Oxford Nanopore reads. 
    Source: https://github.com/MBoemo/DNAscent
    Documentation: https://dnascent.readthedocs.io/en/latest/?badge=latest
    Web: https://www.boemogroup.org/
    Please submit any bugs to https://github.com/MBoemo/DNAscent/issues.

%post

    TZ=Europe/London
    ln -snf /usr/share/zoneinfo/$TZ /etc/localtime && echo $TZ > /etc/timezone
    apt update
    apt install -y tzdata

    # Install system packages
    apt-get update && apt-get install -y \
        lzma-dev \
        build-essential \
        liblzma-dev \
        libbz2-dev \
        libbsd-dev \
        wget \
        git \
        zlib1g-dev \
        libncurses5-dev \
        libgdbm-dev \
        libnss3-dev \
        libssl-dev \
        libreadline-dev \
        libffi-dev \
        libsqlite3-dev \
        python3 \
        python3-pip \
        libboost-all-dev \
        cmake

    # Install conan
    pip3 install "conan<2" build;
    export PATH=$PATH:/opt/python3.9/bin   

    # Clone and compile DNAscent
    mkdir -p /app
    cd app
    git clone --recursive https://github.com/MBoemo/DNAscent.git
    cd DNAscent
    make
    
    # Install vbz plugin
    cd /
    mkdir -p /plugin
    cd plugin
    wget https://github.com/nanoporetech/vbz_compression/releases/download/v1.0.1/ont-vbz-hdf-plugin-1.0.1-Linux-x86_64.tar.gz
    tar -xf ont-vbz-hdf-plugin-1.0.1-Linux-x86_64.tar.gz 
 
   
%environment

    # cuda paths
    export CUDA_HOME=/usr/local/cuda
    export CPATH=/usr/local/cuda/include:$CPATH
    export CUDA_PATH=/usr/local/cuda
    export LIBRARY_PATH=/usr/local/cuda/lib64:$LIBRARY_PATH
    export LD_LIBRARY_PATH=/usr/local/cuda/lib64:$LD_LIBRARY_PATH
    export PATH=/usr/local/cuda/bin:$PATH
    
    # vbz plugin path
    export HDF5_PLUGIN_PATH=/plugin/ont-vbz-hdf-plugin-1.0.1-Linux/usr/local/hdf5/lib/plugin

%runscript
    exec /app/DNAscent/bin/DNAscent "$@"