# The SeqAn Repository¶

This article describes the SeqAn repository structure and how to work with full SeqAn sources.

## Getting Started¶

We assume that you have read Installing SeqAn and have cloned or unzipped the full SeqAn sources to ~/devel/seqan (not the “library sources” described in other places).

SeqAn supports the usual CMake build types and we recommend using multiple build directories. Start like this:

# mkdir -p ~/devel/seqan-build/release
# cd ~/devel/seqan-build/release
# cmake ../../seqan -DCMAKE_BUILD_TYPE=Release


In addition to CMAKE_BUILD_TYPE there is also the SEQAN_BUILD_SYSTEM parameter which can be one of

1. DEVELOP – all build targets (apps, demos, tests) and documentation (dox, manual) are created (the default).
2. SEQAN_RELEASE_LIBRARY – only dox and library targets are created.
3. SEQAN_RELEASE_APPS – all app targets are created, but nothing else.
4. APP:$APPNAME – only a single app target is created for the chosen app. All build systems other than DEVELOP are only relevant to packaging releases. As usual, calling make$TARGET will build a single target and just make will build all targets. On Windows, run cmake --build . --target $TARGET or just cmake --build instead. ## Overview¶ The main repository structure is shown in the following picture. seqan |-- CMakeLists.txt CMake script file. | |-- LICENSE Top-Level Information Files |-- README.rst | |-- apps Applications | |-- demos Demos | |-- dox API documentation system | |-- include/seqan SeqAn header ("the library") | |-- manual Manuals | |-- tests Unit tests for library modules | -- util Miscellaneous and Utility Code  The repository root contains some information files such as the LICENSE and README.rst. The other folders are as follows: ## apps¶ The apps folder contains many applications, and each application directory contains one CMakeLists.txt file and the files for compiling at least one binary. Usually, apps have tests, too. In this case, there is a subdirectory tests. Writing application tests is covered in detail in the article Writing App Tests. The general structure of an app is as follows: seqan/apps/razers |-- CMakeLists.txt CMake script file | |-- README Documentation and License Files |-- LICENSE | |-- example Small Example Files | |-- genome.fa | |-- reads.fa | -- ... | |-- razers.cpp Source Files for Executables |-- razers.h |-- ... | -- tests App Tests Files  Note that some applications have binary names (make targets) that are not identical to the app-name, e.g. yara has yara_mapper and yara_indexer. ## demos¶ The demos are short programs and code snippets that are used in the dox or the manual. They serve as small examples and also functions as additional unit tests. ## dox¶ The SeqAn API documentation is created using a customly-written system called dox. It is very similar to doxygen, you can find out more about the syntax in API Documentation System (dox). You can build the documentation in the dox subfolder of the source folder: ~ # cd ~/devel/seqan/dox dox # ./dox_only.sh  This will build the documentation into the sub directory html. ## include/seqan¶ This is the actual library consisting of multiple modules: include/ |-- seqan/ | |-- basic/ Library Module basic | | |-- aggregate_concept.h | | |-- debug_test_system.h | | -- ... | |-- basic.h | | | |-- sequence/ Library Module sequence | |-- sequence.h | | | -- ... Other Library Modules  On the top level, there is the folder seqan that contains the library modules. Inside the folder seqan, there is one directory and one header for each module. The folder <module-name> contains the headers for the module module-name. The header <module-name>.h includes the headers from the module module-name. Including the header makes the code in the module available. Note Header only library Remember that SeqAn is a template library that consists entirely of headers. No build steps are required for building the library and no shared objects will be created. ## manual¶ The SeqAn manual is created using the Sphinx documentation system. Follow these instructions to set up a local sphinx environment and build the manual: $ virtualenv ~/seqan-manual-env
$source ~/seqan-manual-env/bin/activate (seqan-manual-env)$ cd ~/seqan/manual
(seqan-manual-env) $pip install -r requirements.txt (seqan-manual-env)$ make html


Note that you have to first build the dox documentation since plugins for generating the :dox: links rely on the generated search index for checks. In order to get correct dox-links within the generated manuals, you have to specify the correct branch version. If you are working on the develop branch there is nothing to do, since 'develop' is set by default. But if you are working on another branch, for example master, you can set the correct branch by calling

(seqan-manual-env) \$ export READTHEDOCS_VERSION='master'


before you call make html as described in the previous step. This will generate the correct links to the master’s version of the dox, i.e., http://docs.seqan.de/seqan/master/

## tests¶

The folder tests contains the unit tests for the library modules.

For each library module, there is a directory below tests with the same name that contains the tests for this module. Simpler modules have one tests executable, whereas there might be multiple tests executables for larger modules. For example, the module index has multiple test programs test_index_qgram, test_index_shapes` etc. Writing tests is explained in detail in the article Writing Unit Tests.