install_spacec.sh

#!/bin/bash
set -e

# Function to prompt user for package manager choice
choose_package_manager() {
    read -p "Choose package manager (mamba/conda) [conda]: " pkg_manager
    pkg_manager=${pkg_manager:-conda}
    if [[ "$pkg_manager" != "mamba" && "$pkg_manager" != "conda" ]]; then
        echo "Invalid choice. Defaulting to conda."
        pkg_manager="conda"
    fi
    echo "Using $pkg_manager"
}

# Choose package manager
choose_package_manager

# Create and activate conda environment
$pkg_manager create -n spacec python=3.10 -y
source activate spacec

read -p "Do you want to install the GPU version of SPACEc? (y/n): " confirm
if [ "$confirm" = "y" ]; then
    nvidia-smi
    # Install packages
    $pkg_manager install conda-forge::cudatoolkit=11.2.2 -y
    $pkg_manager install conda-forge::cudnn=8.1.0.77 -y
    $pkg_manager install -c conda-forge graphviz libvips pyvips openslide-python -y

    # Set environment variables
    mkdir -p $CONDA_PREFIX/etc/conda/activate.d
    echo 'export PATH=$CONDA_PREFIX/bin:$PATH' > $CONDA_PREFIX/etc/conda/activate.d/env_vars.sh
    echo 'export LD_LIBRARY_PATH=$CONDA_PREFIX/lib:$LD_LIBRARY_PATH' >> $CONDA_PREFIX/etc/conda/activate.d/env_vars.sh
    chmod +x $CONDA_PREFIX/etc/conda/activate.d/env_vars.sh

    # Install Python packages
    pip install --upgrade pip
    pip install spacec
    pip install pandas==1.*
    pip install protobuf==3.20.0
    pip install numpy==1.24.*
    pip install tensorflow-gpu==2.8.0

    # Install RAPIDS
    read -p "Do you want to install the RAPIDS? NVIDIA RTX20XX or better required! (y/n): " confirm
    if [ "$confirm" = "y" ]; then
        $pkg_manager install -c rapidsai -c conda-forge -c nvidia rapids=24.02 -y #python=3.10 cuda-version=11.2 -y
        pip install rapids-singlecell==0.9.5
        pip install pandas==1.5.*
    else
        echo "RAPIDS installation aborted by the user."
    fi

    echo "Installation complete. Please restart the terminal to apply the changes."
else
    if [[ "$(uname)" == "Darwin" ]]; then
        echo "Configure SPACEc for macOS"
        conda config --env --set subdir osx-64
        $pkg_manager install -c conda-forge graphviz libvips pyvips openslide-python -y
        # Install Python packages
        pip install --upgrade pip
        pip install spacec
        $pkg_manager install tensorflow=2.10.0
        pip uninstall werkzeug -y
        pip install numpy==1.26.4 werkzeug==2.3.8
    else
        echo "Running on Linux"
        $pkg_manager install -c conda-forge graphviz libvips pyvips openslide-python -y
        pip install --upgrade pip
        pip install spacec
        pip install pandas==1.*
        pip install protobuf==3.20.0
        pip install numpy==1.24.*
    fi

    echo "Installation complete. Please restart the terminal to apply the changes."
fi