SeqAn3 3.1.0-rc.2
The Modern C++ library for sequence analysis.
Quick Setup (using CMake)

Learning Objective:
In this short guide you will learn how to set up SeqAn and how to compile a small example to test whether everything works.

DifficultyEasy
Duration30 Minutes
Prerequisite tutorialsNo prerequisites
Recommended reading


Software

Requirements:

  • gcc >= 7
  • cmake >= 3.4
  • git

Installing GCC

SeqAn requires a compiler with full C++20 support or GCC >= 7. Current versions of LLVM/Clang and VisualStudio/MSVC are not yet supported. We will briefly explain how to install GCC-10 (or the latest GCC if such an option is available) on some popular operating systems. We recommend using the latest version of GCC available. For more information, refer to your operating system's documentation.

Linux-based

Ubuntu >= 18.04

sudo apt install g++

Ubuntu < 18.04

sudo add-apt-repository ppa:ubuntu-toolchain-r/test
sudo apt update
sudo apt install g++-10

Using conda

To avoid interference with system packages, we recommend creating a new environment when using conda.

conda create -n conda_gcc_env -c conda-forge gcc_linux-64
conda activate conda_gcc_env

This will put GCC in a separate environment conda_gcc_env which can be activated via conda activate conda_gcc_env and deactivated via conda deactivate.

macOS

Using Homebrew

brew install gcc

Using MacPorts

sudo port install gcc10

Windows

Using WSL

The Windows Subsystem for Linux offers an easy way to run a Linux distribution under Windows. Follow Microsoft's setup guide to install WSL and then follow the steps listed for Linux-based systems.

Browser-based

Using gitpod.io

gitpod.io allows you to edit, compile and run code from within your browser. The free version includes 50 hours of use per month, which is plenty for our tutorials. A GitHub account is required. Click here to open SeqAn3 in gitpod.

Using GitHub codespaces

GitHub offers a service similar to gitpod. Codespaces are currently in public beta and may not be available to everyone. Click here to check for availability.

Please note that you may have to manually clone the submodules by running git submodule update --init.

Attention
After installing, g++ --version should print the desired version. If not, you may have to use, for example, g++-10 --version or even specify the full path to your compiler.

Similarly, you may need to install CMake and git, e.g. apt install cmake git.

Directory Structure

In this section we will use the tree command to show the directory structure. This program may not be installed on your system. If so, you may wish to install it or verify the directory structure in other ways, e.g. by using ls -l.

For this project, we recommend following directory layout:

tutorial
├── source
├── build
└── seqan3

To set these directories up you can follow this script (note the --recurse-submodules when cloning SeqAn3):

mkdir tutorial
cd tutorial
mkdir build
mkdir source
git clone --recurse-submodules https://github.com/seqan/seqan3.git

The output of the command tree -L 2 should now look like this:

.
├── build
├── seqan3
│   ├── build_system
│   ├── CHANGELOG.md
│   ├── ...
│   └── test
└── source
8 directories, 6 files

Compiling and Running

To test whether everything works, we will now compile and run a small example.

First we create the file hello_world.cpp in the source directory with the following contents:

int main()
{
seqan3::debug_stream << "Hello World!\n";
return 0;
}
Provides seqan3::debug_stream and related types.
debug_stream_type debug_stream
A global instance of seqan3::debug_stream_type.
Definition: debug_stream.hpp:37

To compile it, we first create a CMakeLists.txt file in the source directory:

cmake_minimum_required (VERSION 3.4)
project (seqan3_tutorial CXX)
# add seqan3 to search path
list(APPEND CMAKE_PREFIX_PATH "${CMAKE_CURRENT_SOURCE_DIR}/../seqan3/build_system")
# require seqan3 with a version between >=3.0.0 and <4.0.0
find_package (seqan3 3.0 REQUIRED)
# build app with seqan3
add_executable (hello_world hello_world.cpp)
target_link_libraries (hello_world seqan3::seqan3)
The main SeqAn3 namespace.
Definition: cleanup.hpp:4

The directories should now look like this:

.
├── build
├── seqan3
│ ├── build_system
│ ├── CHANGELOG.md
│ ├── ...
│ └── test
└── source
├── CMakeLists.txt
└── hello_world.cpp

Now we can switch to the directory build and run:

cmake -DCMAKE_BUILD_TYPE=Release ../source
make
./hello_world

The output should be Hello World!. Note that the build type is specified with -DCMAKE_BUILD_TYPE=Release. Specifying Release enables an optimized build where no debug information is available. Release mode is therefore suitable for the end user. Programs built using -DCMAKE_BUILD_TYPE=Debug will run slower, but also make the detection of errors easier. Debug is suitable for contributors, and we recommend using it while working with our Tutorials.

Remarks
Depending on the standard C++ compiler on your system, you may need to specify the compiler via -DCMAKE_CXX_COMPILER=, for example:
cmake -DCMAKE_CXX_COMPILER=/path/to/executable/g++-10 ../source

Adding a new source file to your project

If you create a new cpp file and want to compile it, you need to add another add_executable and target_link_libraries directive to you CMakeLists.txt. For example, after adding another_program.cpp your CMakeLists.txt may look like this:

cmake_minimum_required (VERSION 3.4)
project (seqan3_tutorial CXX)
# add seqan3 to search path
list(APPEND CMAKE_PREFIX_PATH "${CMAKE_CURRENT_SOURCE_DIR}/../seqan3/build_system")
# require seqan3 with a version between >=3.0.0 and <4.0.0
find_package (seqan3 3.0 REQUIRED)
# build app with seqan3
add_executable (hello_world hello_world.cpp)
target_link_libraries (hello_world seqan3::seqan3)
add_executable (another_program another_program.cpp)
target_link_libraries (another_program seqan3::seqan3)

Encountered issues

  • Using conda's gcc package: /usr/lib/x86_64-linux-gnu/libstdc++.so.6: version 'CXXABI_1.3.11' not found
    Try setting LD_LIBRARY_PATH:
    export LD_LIBRARY_PATH=<conda_install_path>/envs/conda_gcc_env/lib/
    where <conda_install_path> must be replaced by the path yo your conda installation.
    Usually this corresponds to the path printed by conda info --base and may look similar to /home/user/miniconda3/.
  • Assembler not found: ... could not understand flag m ...
    Try adding /usr/bin to your PATH:
    export PATH=/usr/bin:$PATH
    and run cmake again.