Installation#

Before continuing, please register and download HyPhy.

Once downloaded, install HyPhy as follows:

Navigate to the newly downloaded/cloned HyPhy directory
```
cd hyphy
```
Configure HyPhy using CMake
```
cmake .
```
- By default, HyPhy will be installed into /usr/local/, but it can be installed on any location of your system by specifying a custom installation path:
```
cmake -DINSTALL_PREFIX=/location/of/choice .
```
- If you prefer to use other build systems supported by CMake, such as XCode, configure HyPhy using the generator (-G) switch:
```
cmake -G Xcode .
```
- If would like to specify a particular C/C++ compiler (please note that it must support the C++-14 language standard) for your HyPhy build, use this command:
```
cmake . -DCMAKE_CXX_COMPILER=/path/to/C++-compiler -DCMAKE_C_COMPILER=/path/to/C-compiler
```
If you are building HyPhy under MacOS X, you can specify which version of SDK to use, for example:
```
    cmake -DCMAKE_OSX_SYSROOT=/Developer/SDKs/MacOSX10.9.sdk/ .
```
Build HyPhy by running make with one of the following build targets given below. For example, to install the executable HYPHYMP, you would enter the following command:
```
make MP2
```
- MP2/MP - build a HyPhy executable (HYPHYMP) using OpenMP to support symmetric multiprocessing. If OpenMP is not installed or not supported by the compiler (e.g. LLVM), the compiled executable will not support multi-threading. You can confirm case by examining the output from running cmake. If openMP is installed, you should see something similar to the following in the output:
```
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Success
-- Try OpenMP CXX flag = [-fopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Success
-- Found OpenMP: -fopenmp
```
- MPI - build a HyPhy executable (HYPHYMPI) using the message passing interface MPI to support parallel execution on distributed systems (clusters). An MPI library (e.g., OpenMPI) must be installed and available in your path. You can check if this is the case by examining the output from running cmake. If openMPI is installed, you should see something similar to the following in the output:
```
    -- Found MPI_C: /opt/scyld/openmpi/1.6.3/gnu/lib/libmpi.so;/usr/lib64/libibverbs.so;/usr/lib64/libdat.so;/usr/lib64/librt.so;/usr/lib64/libnsl.so;/usr/lib64/libutil.so;/usr/lib64/libm.so;/usr/lib64/libtorque.so;/usr/lib64/libm.so;/usr/lib64/libnuma.so;/usr/lib64/librt.so;/usr/lib64/libnsl.so;/usr/lib64/libutil.so;/usr/lib64/libm.so

    -- Found MPI_CXX: /opt/scyld/openmpi/1.6.3/gnu/lib/libmpi_cxx.so;/opt/scyld/openmpi/1.6.3/gnu/lib/libmpi.so;/usr/lib64/libibverbs.so;/usr/lib64/libdat.so;/usr/lib64/librt.so;/usr/lib64/libnsl.so;/usr/lib64/libutil.so;/usr/lib64/libm.so;/usr/lib64/libtorque.so;/usr/lib64/libm.so;/usr/lib64/libnuma.so;/usr/lib64/librt.so;/usr/lib64/libnsl.so;/usr/lib64/libutil.so;/usr/lib64/libm.so
```
- LIB - build a HyPhy library (libhyphy_mp), optionally using OpenMP (see above) to support multiprocessing
Finally, install HyPhy on your system with the command
```
make install
```
HyPhy will install either in its default location /usr/local/, or in any custom /location/of/choice/ provided when configuring CMake.
- HYPHYMP(I) will be installed at /location/of/choice/bin
- libhyphy_mp.(so/dylib/dll) will be installed at /location/of/choice/lib
- HyPhy's standard library of scripts/batchfiles will go into /location/of/choice/lib/hyphy