SeqAn App Template

This is a template for C++ app developers. You can easily use this template and modify the existing code to suit your needs. It provides an elementary CMake set-up, some useful SeqAn libraries, and an example application.

For requirements, check the Software section of the SeqAn3 Quick Setup.

Instructions for App Developers:

If you want to build an app, do the following:

0. You need to be signed in with a GitHub account.

1. Press the Use this template-Button to create your own repository.

   
   

   Screenshot TODO

2. Clone your repository locally: git clone [email protected]:max/my-repo-name.git

Note: The subsequent steps are not necessary but a recommendation and quick setup.

3. Adapt the project name in my-repo-name/CMakeLists.txt, e.g., from app-template to MyDragonApp

   
   

   The project name is defined in these lines:

   project (app-template
            LANGUAGES CXX
            VERSION 1.0.0
            DESCRIPTION "My application description"
   )

   Change it e.g. to this:

   project (MyDragonApp
            LANGUAGES CXX
            VERSION 1.0.0
            DESCRIPTION "Let dragons fly"
   )

4. Build and test the app (example)

   
   

   Next to your local repository clone (e.g. my-repo-name), you can do the following to build and test your app:

   mkdir build           # create build directory
   cd build              # step into build directory
   cmake ../my-repo-name # call cmake on the repository
   make                  # build the app MyDragonApp
   make check            # build and run tests *1
   ./bin/MyDragonApp     # Execute the app (prints a short help page)

Instructions for SeqAn3 Tutorial Purposes:

If you just want some hands-on experience with SeqAn Libraries or a quick setup for our tutorials, do the following:

1. Clone this repository: git clone https://github.com/seqan/app-template.git
2. Create a build directory and visit it: mkdir build && cd build
3. Run CMake: cmake ../app-template
4. Build the application: make
5. Try executing the app: ./bin/app-template

You can now start your hands-on experience by looking at or editing the file src/main.cpp.

Adding a new cpp file

If you want to add a new cpp file (e.g., tutorial1.cpp) that is compiled and linked with the current infrastructure, do the following:

1. Create a new file tutorial1.cpp in the src/ directory.

   The file content could look like this:

   
   

   #include <seqan3/core/debug_stream.hpp>
   
   int main()
   {
       seqan3::debug_stream << "Hello, World!" << std::endl;
   }

2. Add the following lines at the bottom of src/CMakeLists.txt

   # Add another cpp file.
   add_executable (tutorial01 tutorial01.cpp)
   target_link_libraries (tutorial01 PRIVATE "${PROJECT_NAME}_lib")

3. Go to the build directory cd build

4. Refresh CMake cmake .

5. Build your new cpp file make tutorial01

6. Execute your new binary with ./tutorial01