longcallR-nn.def

Bootstrap: docker
From: nvidia/cuda:11.6.1-devel-ubuntu20.04

%post
    apt-get update && apt-get install -y wget git curl make gcc g++ parallel libncurses5-dev zlib1g-dev libbz2-dev liblzma-dev

    # create directory for tools
    mkdir -p /tools
    # create directory for work
    mkdir -p /work

    # Install Miniconda
    wget https://repo.anaconda.com/miniconda/Miniconda3-py38_23.11.0-2-Linux-x86_64.sh -O /tools/miniconda3.sh
    bash /tools/miniconda3.sh -b -p /tools/miniconda3
    rm /tools/miniconda3.sh

    # Initialize conda and add it to the PATH
    export PATH=/tools/miniconda3/bin:$PATH
    /tools/miniconda3/bin/conda init bash
    /tools/miniconda3/bin/conda create -n pytorch python=3.9 -y

    # Install longcallR-nn
    git clone https://github.com/huangnengCSU/longcallR-nn.git /tools/longcallR-nn
    cd /tools/longcallR-nn
    /tools/miniconda3/bin/conda run -n pytorch pip install -r requirements.txt
    /tools/miniconda3/bin/conda run -n pytorch pip install .

    # Install torch-gpu
    /tools/miniconda3/bin/conda run -n pytorch conda install pytorch==1.13.1 torchvision==0.14.1 torchaudio==0.13.1 pytorch-cuda=11.6 torchmetrics -c pytorch -c nvidia -y
    # Install torch-cpu
    # conda install pytorch torchvision torchaudio torchmetrics cpuonly -c pytorch -y


    # Install Rust
    curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh -s -- -y
    export PATH=$HOME/.cargo/bin:$PATH

    # Compile longcallR-dp
    cd /tools/longcallR-nn/longcallR_dp
    cargo build --release
    export PATH=/tools/longcallR-nn/longcallR_dp/target/release:$PATH

    # Clean up
    apt-get clean
    /tools/miniconda3/bin/conda clean -a -y

%environment
    export PATH=/tools/miniconda3/bin:$PATH
    . /tools/miniconda3/bin/activate pytorch
    export PATH=$HOME/.cargo/bin:$PATH
    export PATH=/tools/longcallR-nn/longcallR_dp/target/release:$PATH


# %runscript
#     cd /work
#     echo "longcallR-nn"
#     longcallR-nn call -h