Building emDNA

emDNA supports the following systems:

The code base has virtually no system-dependent code so emDNA can most likely be built on any platforms that provide a recent C++ compiler (with C++11/14 support) but this is not tested nor validated.

Table of Contents

Requirements

Note that, emDNA has only been tested on the following platform/compiler setups:

It is very likely that the project can be built on other setups (e.g. GCC+MinGW on Windows) but this has not been tested.

Cloning the repository

emDNA includes various dependencies as submodule so the --recursive option is recommended when cloning the repository:

git clone --recursive git@github.com:nicocvn/emDNA.git emDNA.git

Build instructions

The following notes assume the emDNA repository was cloned in the directory /somewhere/emDNA.git (C:\somewhere\emDNA.git on Windows) so adapt the various paths used in the commands.

Note: because the project is based on CMake it is possible to pass additional compiler flags if desired but this is not covered in the instructions.

macOS and Ubuntu

  1. Create build and installation directories:

     $ cd /somewhere
 $ mkdir emDNA-build emDNA-install

  2. Configure the CMake project:

     $ cmake -S emDNA.git/ -B emDNA-build/ -DCMAKE_BUILD_TYPE=Release

    You can change the value of -DCMAKE_BUILD_TYPE but the recommended one is Release.

  3. Build the project

     $ cmake --build emDNA-build/ --config Release --parallel 2

    The value 2 used for --parallel indicates the number of jobs to use for the build process and it can be increased based on the number of cores/CPUs available on the system.

  4. Install:

     $ cmake --install emDNA-build/ --config Release --prefix emDNA-install/

    This will install the various emDNA command-line tools in /somewhere/emDNA-install/bin/Release (or whatever build type was selected during configuration). The tools can then be moved/copied elsewhere.

  5. Cleanup: the build directory can be removed once the install step was completed successfully.

Windows

  1. Start a developer command prompt: this should be available as Developer PowerShell 2019 from the start menu (the year might be different depending on the installed Visual Studio version).

  2. Create build and installation directories:

     PS > cd C:\somewhere
 PS > mkdir emDNA-build
 PS > mkdir emDNA-install

  3. Configure the CMake project:

     PS >  cmake -G"Visual Studio 16 2019" -A x64 -S .\emDNA.git\ -B .\emDNA-build\ -DCMAKE_BUILD_TYPE=Release

    The "Visual Studio 16 2019" value might need to be adapted depending on the CMake and Visual Studio versions available on the system. Executing the command cmake -G will list the available generators values.

  4. Build the project:

     PS > cmake --build .\emDNA-build\ --config Release --parallel 2

  5. Install:

     PS > cmake --install .\emDNA-build\ --config Release --prefix .\emDNA-install\

    This will install the various emDNA command-line tools in C:\somewhere\emDNA-install\bin\Release (or whatever build type was selected during configuration). The tools can then be moved/copied elsewhere.

  6. Cleanup: the build directory can be removed once the install step was completed successfully.

Note: the emDNA command line tools can be run from a regular command prompt after being installed; there is no need to start a developer command prompt to run them.

Running the tests

The building and installation process creates two executables that run a set of unit tests on different components of the software:

It is recommended to run these two executables and make sure all tests are successful (e.g. no failure messages).