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. See GitHub's documentation for more information.
2. Wait for GitHub actions to create a commit in your new repository. The commit message will be Initialise repository and it will replace placeholders in the code. Afterwards, the README in your repository will be customised to your repository, among other things.

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⚠️ Important ⚠️

From here on out, follow the instructions in your repository.

You will probably need to reload your repository page to see the changes.

The instructions below are for the template repository and will not work for your repository.

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3. Clone your repository locally: git clone [email protected]:seqan/app-template.git

4. Build and test the app (example)

   In your local repository clone, you can do the following to build and test your app:

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

Setting up Codecov (optional)

1. Go to https://codecov.io/gh/seqan/app-template.
2. Sign in with your GitHub account.
3. Go to https://app.codecov.io/gh/seqan/app-template/config/general.
   If the repository cannot be found, go to https://app.codecov.io/gh/seqan and click Resync.
   Then try again.
4. Copy the Repository Upload Token.
5. Go to https://github.com/seqan/app-template/settings/secrets/actions.
6. Add a New repository secret with the name CODECOV_TOKEN and the value of the Repository Upload Token.
7. Done! The next push to your repository will create a Codecov report.

Setting up permissions for Lint action (optional)

1. Go to https://github.com/seqan/app-template/settings/actions.
2. Under Workflow permissions, at the very bottom, tick Allow GitHub Actions to create and approve pull requests and click Save.
3. You can go to https://github.com/seqan/app-template/actions/workflows/lint.yml and click Run workflow to run linting.

Instructions for SeqAn3 Tutorial Purposes:

If you just some quick hands-on experience with SeqAn Libraries, you can also just clone this repository and start editing the src/main.cpp file.

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