FastANI build and installation guide
====================================

Requirements
------------

- CMake 3.2 or newer
- A C++11 compiler with OpenMP support
  - GCC >= 4.8 on Linux
  - Clang >= 3.3 on macOS
- Zlib
- One of:
  - GNU Scientific Library (GSL)
  - Boost

macOS note:
- If you build with Clang, install `libomp` so OpenMP is available.


Recommended performance build
-----------------------------

For best runtime performance, build FastANI in `Release` mode:

```sh
rm -rf build
cmake -S . -B build -DCMAKE_BUILD_TYPE=Release
cmake --build build -j
```

This default release build favors portability across machines. If you want a
host-optimized local benchmark build, enable:

```sh
cmake -S . -B build -DCMAKE_BUILD_TYPE=Release -DFASTANI_NATIVE_OPTIMIZATION=ON
```

This produces the executable at:

```text
build/fastANI
```

If you want debug symbols while still keeping optimized code for benchmarking,
you can use:

```sh
rm -rf build
cmake -S . -B build -DCMAKE_BUILD_TYPE=RelWithDebInfo
cmake --build build -j
```


Install to a prefix
-------------------

To install FastANI under a specific prefix:

```sh
rm -rf build
cmake -S . -B build -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=/path/to/install
cmake --build build -j
cmake --install build
```

This installs the executable to:

```text
/path/to/install/bin/fastANI
```

If you do not set `CMAKE_INSTALL_PREFIX`, the default is typically `/usr/local`,
which may require elevated privileges during installation.


Dependency configuration
------------------------

If CMake cannot find GSL or Boost automatically, you can provide paths
explicitly during configuration.

Examples:

```sh
cmake -S . -B build -DCMAKE_BUILD_TYPE=Release -DGSL_ROOT_DIR=/path/to/gsl
```

```sh
cmake -S . -B build -DCMAKE_BUILD_TYPE=Release -DBOOST_ROOT=/path/to/boost
```


Useful CMake options
--------------------

`-DCMAKE_INSTALL_PREFIX=/path/to/install`
- Install prefix used by `cmake --install build`.

`-DGSL_ROOT_DIR=/path/to/gsl`
- Location of a non-default GSL installation.

`-DGSL_SHARED=OFF`
- Statically link GSL instead of dynamically.

`-DBOOST_ROOT=/path/to/boost`
- Use Boost from this location instead of GSL discovery defaults.

`-DBUILD_TESTING=ON`
- Build the test suite. This requires initializing submodules first with
  `git submodule update --init --recursive`.

`-DFASTANI_NATIVE_OPTIMIZATION=ON`
- Add `-march=native` for host-optimized local builds. This can improve speed on
  the current machine, but it reduces portability and can make binaries harder to
  compare across systems.


Notes
-----

- `Release` builds are recommended for actual performance evaluation.
- Fresh clones build the `fastANI` executable by default without requiring test
  submodules.
- If you want to build tests, initialize submodules first and configure with
  `-DBUILD_TESTING=ON`.
- If you are running directly from the build tree, invoke `build/fastANI`.
- If you install FastANI, you can invoke it as `fastANI` once the install
  prefix `bin/` directory is on your `PATH`.