setup.bat

@echo off
REM WGS Extract v6 Setup Script (Windows)
REM Sets up virtual environment and installs all dependencies

setlocal enabledelayedexpansion

echo.
echo ================================================================
echo            WGS Extract v6 - Setup Script (Windows)
echo ================================================================
echo.

REM Check Python version
echo 1. Checking Python version...
where python >nul 2>nul
if %ERRORLEVEL% NEQ 0 (
    echo    X Error: python not found
    echo      Please install Python 3.13 or later
    pause
    exit /b 1
)

for /f "tokens=2" %%i in ('python --version 2^>^&1') do set PYTHON_VERSION=%%i
echo    * Found Python %PYTHON_VERSION%
echo.

REM Check external tools
echo 2. Checking external tools...
set MISSING_TOOLS=

where samtools >nul 2>nul
if %ERRORLEVEL% NEQ 0 set MISSING_TOOLS=!MISSING_TOOLS! samtools

where bcftools >nul 2>nul
if %ERRORLEVEL% NEQ 0 set MISSING_TOOLS=!MISSING_TOOLS! bcftools

where tabix >nul 2>nul
if %ERRORLEVEL% NEQ 0 set MISSING_TOOLS=!MISSING_TOOLS! tabix

where java >nul 2>nul
if %ERRORLEVEL% NEQ 0 set MISSING_TOOLS=!MISSING_TOOLS! java

if not "!MISSING_TOOLS!"=="" (
    echo    ! Warning: Missing tools:!MISSING_TOOLS!
    echo      Install from: https://github.com/samtools/samtools/releases
    echo      Java: https://adoptium.net/
    echo.
    set /p CONTINUE="   Continue anyway? (y/n) "
    if /i not "!CONTINUE!"=="y" exit /b 1
) else (
    echo    * All external tools found
)
echo.

REM Create virtual environment
echo 3. Creating virtual environment...
if exist venv (
    echo    ! venv\ already exists
    set /p RECREATE="   Remove and recreate? (y/n) "
    if /i "!RECREATE!"=="y" (
        rmdir /s /q venv
        python -m venv venv
        echo    * Virtual environment recreated
    ) else (
        echo    * Using existing virtual environment
    )
) else (
    python -m venv venv
    echo    * Virtual environment created
)
echo.

REM Activate virtual environment
echo 4. Activating virtual environment...
call venv\Scripts\activate.bat
echo    * Virtual environment activated
echo.

REM Upgrade pip
echo 5. Upgrading pip...
python -m pip install --upgrade pip >nul 2>&1
echo    * pip upgraded
echo.

REM Install requirements
echo 6. Installing WGS Extract dependencies...
pip install -r requirements.txt
echo    * Dependencies installed
echo.

REM Install Yleaf
echo 7. Installing bundled Yleaf...
if exist yleaf (
    pip install ./yleaf/
    echo    * Yleaf installed from ./yleaf/
) else (
    echo    X Error: yleaf\ directory not found
    pause
    exit /b 1
)
echo.

REM Verify installation
echo 8. Verifying installation...

python -c "import wgsextract; print('WGS Extract:', wgsextract.__version__)" >nul 2>&1
if %ERRORLEVEL% EQU 0 (
    echo    * WGS Extract modules OK
) else (
    echo    X WGS Extract import failed
    pause
    exit /b 1
)

python -c "import yleaf; print('Yleaf:', yleaf.__version__)" >nul 2>&1
if %ERRORLEVEL% EQU 0 (
    echo    * Yleaf OK
) else (
    echo    X Yleaf import failed
    pause
    exit /b 1
)

where Yleaf >nul 2>&1
if %ERRORLEVEL% EQU 0 (
    echo    * Yleaf command OK
) else (
    echo    X Yleaf command failed
    pause
    exit /b 1
)

echo.
echo ================================================================
echo                     Setup Complete!
echo ================================================================
echo.
echo To run WGS Extract:
echo   wgsextract.bat
echo.
echo First time users:
echo   1. Load a BAM/CRAM file from Settings tab
echo   2. Download reference genomes (Settings -^> Reference Library)
echo   3. Explore features in Extract Data and Analyze tabs
echo.
pause