Installation

This guide covers how to build and install genogrove for use in your projects.

Prerequisites

Before building genogrove, ensure you have:

• C++20 compatible compiler - GCC 13 or newer - Clang 16 or newer - Apple Clang 15 or newer

• CMake 3.14 or higher

• htslib (for compressed file support) - On Ubuntu/Debian: sudo apt-get install libhts-dev - On macOS with Homebrew: brew install htslib - On other systems: Build from source at samtools/htslib

Building from Source

1. Clone the repository:

   git clone https://github.com/genogrove/genogrove.git
   cd genogrove
   

2. Create a build directory and configure:

   cmake -S . -B build -DCMAKE_BUILD_TYPE=Release
   cmake --build build
   

3. (Optional) Run tests:

   # Tests are built when -DBUILD_TESTING=ON
   cmake -S . -B build -DCMAKE_BUILD_TYPE=Release -DBUILD_TESTING=ON
   cmake --build build
   cd build
   ctest -C Release
   

Using in Your Project

CMake Integration

If you’re using CMake, add genogrove to your project:

Option 1: Install system-wide

# From the build directory
sudo cmake --install .

Then in your CMakeLists.txt:

find_package(genogrove REQUIRED)

add_executable(my_program main.cpp)
target_link_libraries(my_program genogrove::genogrove)

Option 2: Add as subdirectory

add_subdirectory(external/genogrove)

add_executable(my_program main.cpp)
target_link_libraries(my_program genogrove::genogrove)

Option 3: Use FetchContent

include(FetchContent)

FetchContent_Declare(
    genogrove
    GIT_REPOSITORY https://github.com/genogrove/genogrove.git
    GIT_TAG main  # or specific version tag
)
FetchContent_MakeAvailable(genogrove)

add_executable(my_program main.cpp)
target_link_libraries(my_program genogrove::genogrove)

Manual Integration

If not using CMake:

1. Add the include directory to your include path:

   # Example with g++
   g++ -std=c++20 -I/path/to/genogrove/include main.cpp -lhts -o my_program
   

2. Link against required libraries: - htslib (-lhts) - pthread (-lpthread) on Linux

Verify Installation

Create a simple test program:

#include <genogrove/data_type/interval.hpp>
#include <iostream>

namespace gdt = genogrove::data_type;

int main() {
    gdt::interval iv{100, 200};
    std::cout << "Genogrove is working! Interval: "
              << iv.to_string() << std::endl;
    return 0;
}

Compile and run:

g++ -std=c++20 test.cpp -o test
./test
# Output: Genogrove is working! Interval: [100, 200]

Development Build

For development with debugging symbols and sanitizers:

cmake -S . -B build-debug \
    -DCMAKE_BUILD_TYPE=Debug \
    -DBUILD_TESTING=ON \
    -DENABLE_SANITIZER=ON
cmake --build build-debug

See SANITIZERS.md in the repository for more information on using AddressSanitizer and UndefinedBehaviorSanitizer.

Troubleshooting

htslib not found

If CMake cannot find htslib:

# Specify htslib location manually
cmake -S . -B build -DHTSLIB_ROOT=/path/to/htslib

C++20 features not available

Ensure your compiler supports C++20:

# Check GCC version
g++ --version  # Should be 13+

# Check Clang version
clang++ --version  # Should be 16+

Build fails on older systems

Consider using a newer compiler via devtoolset (RHEL/CentOS) or a PPA (Ubuntu):

# Ubuntu example
sudo add-apt-repository ppa:ubuntu-toolchain-r/test
sudo apt update
sudo apt install gcc-13 g++-13
export CXX=g++-13

Next Steps

Once installed, proceed to the next sections of the user guide to learn how to use genogrove effectively.