herro-singularity.def

Bootstrap: docker
From: nvidia/cuda:11.7.1-cudnn8-runtime-ubuntu22.04
Stage: devel

%files
    * /herro/

%post
    # Get essential packages
    apt-get update
    apt-get install -y wget git unzip curl build-essential zlib1g-dev zstd

    # Build minimap2
    git clone https://github.com/lh3/minimap2.git && cd minimap2 && make
    cd /

    # Download rustc
    curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh -s -- -y
    export PATH="/root/.cargo/bin:${PATH}"

    # Get libtorch
    wget -q -O libtorch.zip https://download.pytorch.org/libtorch/cu117/libtorch-cxx11-abi-shared-with-deps-2.0.1%2Bcu117.zip
    unzip -q libtorch.zip && rm libtorch.zip
    export LIBTORCH=/libtorch
    export LD_LIBRARY_PATH=${LIBTORCH}/lib:$LD_LIBRARY_PATH

    # build
    cd herro
    RUSTFLAGS="-Ctarget-cpu=native" cargo build -q --release


Bootstrap: docker
From: nvidia/cuda:11.7.1-cudnn8-runtime-ubuntu22.04
Stage: final

%files from devel
    /minimap2/minimap2 /bin/minimap2
    /herro/target/release/herro /bin/herro
    /libtorch /libs/

%environment
    export LIBTORCH=/libs/libtorch
    export LD_LIBRARY_PATH=${LIBTORCH}/lib:$LD_LIBRARY_PATH

%post
    # Get essential packages
    apt-get update
    apt-get install -y libgomp1 zlib1g-dev zstd

%runscript
    herro "$@"

%labels
    Author Dominik Stanojevic
    Version v0.2.0
    Name herro