install.sh

#!/bin/bash

set -e  # Exit immediately if a command fails

# Default flag value
cpu=0
no_modeller=0

# Parse command-line arguments
for arg in "$@"; do
    case $arg in
        --cpu)
        cpu=1
        shift
        ;;
        --no_modeller)
        no_modeller=1
        shift
        ;;
        *)
        # ignore other arguments
        ;;
    esac
done

# Define an error handler function
error_handler() {
    echo "========================================="
    echo "⚠ An error occurred during the installation process."
    echo "If it is a GPU related issue, please adjust your CUDA and CUDNN version in .yml files."
    echo "You can ignore --> fatal: destination path 'ProteinMPNN' already exists and is not an empty directory."
    echo "Please open an issue on our GitHub. We try to fix it in 24 hours!"
    echo "GitHub: https://github.com/soedinglab/PMGen/issues"
    echo "========================================="
    exit 1
}

# Trap any error and call the error handler
trap 'error_handler' ERR

CURRENT_DIR=$(pwd)
ENV_NAME="PMGen"
ENV_FILE="PMGen.yml"
if [ "$cpu" -eq 1 ]; then
    echo "⚡ CPU-only mode activated"
    ENV_FILE="PMGen-cpuonly.yml"
fi
AFFINE_ZIP_URL="https://owncloud.gwdg.de/index.php/s/M1YQOgKxLbVjO0G/download"
AFFINE_FOLDER="AFfine"
AFFINE_ZIP_NAME="$AFFINE_FOLDER/AFfine.zip"
PANDORA_MODIF_PATH="$CURRENT_DIR/PANDORA/PANDORA/Pandora/Modelling_functions.py"
PANDORA_PMHC_PATH="$CURRENT_DIR/PANDORA/PANDORA/PMHC/PMHC.py"

echo "========================================="
echo " Starting Installation: PMGen"
echo " Thank you for using our tool!"
echo "========================================="

# Step 0: Display References
echo "### References for the tools used in this pipeline ###"
echo "1. PANDORA - GitHub: https://github.com/X-lab-3D/PANDORA"
echo "   Paper: https://www.frontiersin.org/articles/10.3389/fimmu.2022.878762/full"
echo "2. AFfine - GitHub: https://github.com/phbradley/alphafold_finetune"
echo "   Paper: https://www.pnas.org/doi/abs/10.1073/pnas.2216697120"
echo "3. Modeller - Website: https://salilab.org/modeller/"
echo "   Paper: A. Fiser, R.K. Do, & A. Sali. Modeling of loops in protein structures, Protein Science 9. 1753-1773, 2000."
echo "4. AlphaFold - GitHub: https://github.com/google-deepmind/alphafold"
echo "   Paper: https://www.nature.com/articles/s41586-021-03819-2"
echo "5. ProteinMPNN - Github https://github.com/dauparas/ProteinMPNN"
echo "   Paper: https://www.science.org/doi/10.1126/science.add2187"
echo "########################################################"

# Step 1: Ask for Modeller License Key
if [ "$no_modeller" -eq 1 ]; then
    echo "⚡ No Modeller version being installed"
    KEY_MODELLER="NOMODELLERKEY"
    export KEY_MODELLER="$KEY_MODELLER"
    echo "✔ Modeller license key has been set to NOMODELLERKEY."
else
    echo -n "Please enter your Modeller license key: "
    read -r KEY_MODELLER
    export KEY_MODELLER="$KEY_MODELLER"
    echo "✔ Modeller license key has been set."
fi

# Step 2: Check if mamba exists; otherwise, use conda
if command -v mamba &>/dev/null; then
    echo "✔ Mamba found and using it"
    CONDA_CMD="mamba"
    ACTIVATE_CMD="conda activate"
else
    CONDA_CMD="conda"
    ACTIVATE_CMD="conda activate"
    echo "⚠ Mamba not found! Falling back to Conda."
fi
# Step 3: Ensure Conda is initialized
if [ -z "$CONDA_PREFIX" ]; then
    source "$(conda info --base)/etc/profile.d/conda.sh"
fi

# Step 4: Create and activate Conda/Mamba environment
echo "✔ Creating and activating environment: $ENV_NAME..."

if ! conda env list | grep -q "$ENV_NAME"; then
    if [ -f "$ENV_FILE" ]; then
        echo "✔ Found $ENV_FILE. Creating environment with dependencies..."
        $CONDA_CMD env create -f "$ENV_FILE"
    else
        echo "⚠ No $ENV_FILE found."
    fi
else
    echo "✔ Environment $ENV_NAME already exists."
fi

# Activate the environment
$ACTIVATE_CMD "$ENV_NAME"

# Step 5: Clone and Install PANDORA
#echo "✔ Cloning and installing PANDORA..."
#if [ ! -d "PANDORA" ]; then
#    git clone https://github.com/X-lab-3D/PANDORA.git
#fi
cd PANDORA
pip install -e .
cd ..
# Step 6: Ensure dependencies are correctly set after installing PANDORA
echo "✔ Reinstalling dependencies to match $ENV_FILE..."
$CONDA_CMD env update -f "$CURRENT_DIR/$ENV_FILE"

# Step 7: Fetch PANDORA Data
echo "✔ Fetching PANDORA data..."
pandora-fetch

# Step 8: Download and Extract AFfine Data
echo "✔ Downloading AFfine data ..."
cd "$CURRENT_DIR"

if [ -d "$AFFINE_FOLDER" ]; then
    echo "✔ AFfine folder found."
    # Download zip to AFfine/
    wget -O "$AFFINE_ZIP_NAME" "$AFFINE_ZIP_URL"
    # Unzip into AFfine/, creating AFfine/af_params/
    unzip -o "$AFFINE_ZIP_NAME" -d "$AFFINE_FOLDER"
    echo "✔ AFfine data extracted into '$AFFINE_FOLDER/af_params/'."
else
    echo "❌ AFfine folder not found. Please clone the git repository properly."
fi

# Step 10: Dowlnload modified files for PANDORA
#echo "Change modified scripts in PANDORA"
#rm "$PANDORA_MODIF_PATH"
#rm "$PANDORA_PMHC_PATH"
#mv "data/modified_files/Modelling_functions.py" "$PANDORA_MODIF_PATH"
#mv "data/modified_files/PMHC.py" "$PANDORA_PMHC_PATH"

# Step 11: Install ProteinMPNN
echo "ProteinMPNN installation"
git clone https://github.com/dauparas/ProteinMPNN.git
echo "✔ ProteinMPNN setup is done. "
# Step 12: Cleanup and Completion
cd "$CURRENT_DIR"
echo "✔ Installation completed successfully!"
echo "Please check and modify 'user_setting.py' file to customize for your usage"
echo "If you want to use NetMHCpan predictions for Anchor, please make sure to install it and provide its path to 'user_setting.py'"
echo "To use PMGen, run: 'conda activate PMGen' "
echo "========================================="
echo "✅ PMGen-MHC is ready to use!"