install.bat

@echo off
REM Installation script for WGS Extract v6 (Windows)

setlocal enabledelayedexpansion

echo ==================================================
echo WGS Extract v6 - Installation (Windows)
echo ==================================================
echo.

REM Check if Python is installed
where python >nul 2>nul
if %ERRORLEVEL% NEQ 0 (
    echo Error: Python is not installed or not in PATH
    echo Please install Python 3.13 or later from https://www.python.org/
    pause
    exit /b 1
)

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

REM Check for BWA
where bwa >nul 2>nul
if %ERRORLEVEL% NEQ 0 (
    echo Warning: BWA not found
    echo BWA is required for alignment operations
    echo Download from: https://github.com/lh3/bwa/releases
    echo.
) else (
    echo BWA found
    echo.
)

REM Check if venv exists
if exist venv (
    echo Virtual environment already exists
    set /p RECREATE="Recreate it? (y/N): "
    if /i "!RECREATE!"=="y" (
        rmdir /s /q venv
        python -m venv venv
    )
) else (
    echo Creating Python virtual environment...
    python -m venv venv
)

echo.

REM Activate virtual environment
echo Activating virtual environment...
call venv\Scripts\activate.bat

REM Upgrade pip
echo Upgrading pip...
python -m pip install --upgrade pip wheel setuptools

echo.

REM Install dependencies
echo Installing dependencies...
pip install -r requirements.txt

echo.

REM Ask about dev dependencies
set /p INSTALL_DEV="Install development dependencies? (y/N): "
if /i "%INSTALL_DEV%"=="y" (
    pip install -r requirements-dev.txt
)

echo.

REM Install package
echo Installing WGS Extract...
pip install -e .

echo.

REM Create directories
echo Creating directories...
if not exist reference\genomes mkdir reference\genomes
if not exist reference\liftover mkdir reference\liftover
if not exist reference\microarray_templates mkdir reference\microarray_templates
if not exist output mkdir output
if not exist temp mkdir temp

echo.

REM Create launcher batch file
echo Creating launcher...
(
echo @echo off
echo call "%~dp0venv\Scripts\activate.bat"
echo python -m wgsextract %%*
) > run_wgsextract.bat

echo.
echo ==================================================
echo Installation complete!
echo ==================================================
echo.
echo To run WGS Extract:
echo   1. Activate virtual environment:
echo      venv\Scripts\activate.bat
echo   2. Run the application:
echo      python -m wgsextract
echo.
echo Or use the launcher:
echo      run_wgsextract.bat
echo.
echo For help:
echo      python -m wgsextract --help
echo.
pause