#!/usr/bin/env bash
set -uo pipefail

echo "==> Installing system tools (samtools, minimap2)"
apt-get update -qq && apt-get install -y -qq --no-install-recommends samtools 2>/dev/null && \
    echo "     samtools installed: $(samtools --version | head -1)" || \
    { echo "     ERROR: samtools installation failed"; exit 1; }

MINIMAP2_DEST="/usr/local/bin/minimap2"
MINIMAP2_URL="https://github.com/lh3/minimap2/releases/download/v2.28/minimap2-2.28_x64-linux.tar.bz2"
if [ -x "$MINIMAP2_DEST" ]; then
    echo "     minimap2 already present: $($MINIMAP2_DEST --version 2>&1 | head -1)"
else
    curl -fSL "$MINIMAP2_URL" | tar xjf - -C /tmp && \
        cp /tmp/minimap2-2.28_x64-linux/minimap2 "$MINIMAP2_DEST" && \
        chmod +x "$MINIMAP2_DEST" && rm -rf /tmp/minimap2* && \
        echo "     minimap2 installed: $($MINIMAP2_DEST --version 2>&1 | head -1)" || \
        { echo "     ERROR: minimap2 installation failed"; exit 1; }
fi

echo "==> Verifying native tools"
samtools --version | head -1
minimap2 --version 2>&1 | head -1

echo "==> Installing Python dependencies"
pip install -r requirements.txt

echo "==> Downloading AutoDock Vina binary …"
VINA_DEST="/usr/local/bin/vina"
VINA_URL="https://github.com/ccsb-scripps/AutoDock-Vina/releases/download/v1.2.7/vina_1.2.7_linux_x86_64"
curl -fSL -o "$VINA_DEST" "$VINA_URL" && chmod +x "$VINA_DEST" && echo "     vina installed at $VINA_DEST ($(stat -c%s "$VINA_DEST") bytes)" || echo "     WARNING: vina download failed — Python fallback will handle"

echo "==> Build complete"