genomifyseq/setup.sh at main · garrettc00per/genomifyseq · GitHub

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#!/bin/bash
set -e

echo "============================================"
echo "   RNA-seq Processing App Setup"
echo "============================================"
echo ""

# Get the directory where this script is located
SCRIPT_DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
cd "$SCRIPT_DIR"

# Local Miniforge installation path (keeps everything self-contained)
MINIFORGE_DIR="$SCRIPT_DIR/.miniforge"

# Function to install Miniforge locally
install_miniforge() {
    echo "Installing Miniforge locally..."
    echo ""

    # Detect architecture
    ARCH=$(uname -m)
    if [ "$ARCH" = "arm64" ]; then
        MINIFORGE_URL="https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-MacOSX-arm64.sh"
    else
        MINIFORGE_URL="https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-MacOSX-x86_64.sh"
    fi

    echo "Downloading Miniforge for $ARCH..."
    curl -L -o /tmp/miniforge.sh "$MINIFORGE_URL"

    echo ""
    echo "Installing to $MINIFORGE_DIR..."
    bash /tmp/miniforge.sh -b -p "$MINIFORGE_DIR"
    rm /tmp/miniforge.sh

    echo ""
    echo "✓ Miniforge installed successfully"
}

# Check for conda/mamba
if [ -d "$MINIFORGE_DIR" ]; then
    # Use local installation
    source "$MINIFORGE_DIR/etc/profile.d/conda.sh"
    source "$MINIFORGE_DIR/etc/profile.d/mamba.sh" 2>/dev/null || true
    CONDA_CMD="mamba"
    echo "✓ Using local Miniforge installation"
elif command -v mamba &> /dev/null; then
    CONDA_CMD="mamba"
    echo "✓ Found system mamba"
elif command -v conda &> /dev/null; then
    CONDA_CMD="conda"
    echo "✓ Found system conda"
else
    echo "Conda/Mamba not found. Installing Miniforge..."
    echo ""
    install_miniforge

    # Source the newly installed conda
    source "$MINIFORGE_DIR/etc/profile.d/conda.sh"
    source "$MINIFORGE_DIR/etc/profile.d/mamba.sh"
    CONDA_CMD="mamba"
fi

# Create/update the conda environment
ENV_NAME="rnaseq_app"

if $CONDA_CMD env list | grep -q "^${ENV_NAME} "; then
    echo ""
    echo "Updating existing environment '$ENV_NAME'..."
    $CONDA_CMD env update -n $ENV_NAME -f environment.yml
else
    echo ""
    echo "Creating new environment '$ENV_NAME'..."
    echo "This may take a few minutes..."
    echo ""
    $CONDA_CMD env create -f environment.yml
fi

# Create necessary directories
mkdir -p data/uploads
mkdir -p data/indices
mkdir -p data/results

# Create a launcher script
cat > "$SCRIPT_DIR/run_app.sh" << 'EOF'
#!/bin/bash
SCRIPT_DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"

# Source conda from local or system installation
if [ -d "$SCRIPT_DIR/.miniforge" ]; then
    source "$SCRIPT_DIR/.miniforge/etc/profile.d/conda.sh"
else
    # Try to find system conda
    if [ -f "$HOME/miniforge3/etc/profile.d/conda.sh" ]; then
        source "$HOME/miniforge3/etc/profile.d/conda.sh"
    elif [ -f "$HOME/miniconda3/etc/profile.d/conda.sh" ]; then
        source "$HOME/miniconda3/etc/profile.d/conda.sh"
    elif [ -f "/opt/homebrew/Caskroom/miniforge/base/etc/profile.d/conda.sh" ]; then
        source "/opt/homebrew/Caskroom/miniforge/base/etc/profile.d/conda.sh"
    fi
fi

conda activate rnaseq_app
cd "$SCRIPT_DIR"
streamlit run app.py
EOF

chmod +x "$SCRIPT_DIR/run_app.sh"

echo ""
echo "============================================"
echo "   Setup Complete!"
echo "============================================"
echo ""
echo "To run the app, simply execute:"
echo ""
echo "  ./run_app.sh"
echo ""
echo "The app will open automatically in your web browser."
echo ""