Integration with your own Build System ¶

This page gives an example of how to use SeqAn in your application based on your own Makefiles. You should be able to adapt the descriptions to configure your build system and/or IDE.

Tip

SeqAn is a header-only library.

Simply adding its include folder to your include path or installing it globally makes it available to your program.

C++14 Standard ¶

On GNU/Linux, BSD and macOS, always add -std=c++14 (or a newer standard) when building on the command line.

For XCode on macOS you need to set this option in the project settings.

As of Visual Studio 2015 our subset of C++14 is already available in all supported compilers.

OpenMP ¶

On GNU/Linux, BSD and macOS, add -fopenmp unless you are using Clang versions older than 3.8.0.

For XCode on macOS OpenMP is not yet available.

With Visual Studio OpenMP is switched on by default.

Operating System specifics ¶

GNU/Linux ¶

Libraries

Add -lrt -lpthread to the compiler call.

BSD ¶

Libraries

Add -lpthread -lexecinfo -lelf to the compiler call.

Misc

Also define -D_GLIBCXX_USE_C99=1 if you are using gcc-4.9.

Warning levels ¶

It is recommended to compile your programs with as many warnings enabled as possible. This section explains which flags to set for different compilers.

GCC, Clang, ICC (unix)¶

The following flags are recommended:

-W -Wall -pedantic: Maximal sensitivity of compiler against possible problems.

Visual Studio ¶

For Visual Studio, the following flags are recommended:

/W2 /wd4996 -D_CRT_SECURE_NO_WARNINGS

Explanation:

/W2: Warning level 2 is pretty verbose already. In the future, we will support level 3 without warnings in SeqAn code.
/wd4996: Allows the use of some deprecated functions without warnings.
-D_CRT_SECURE_NO_WARNINGS ::``: Some C functions like sprintf are prone to incorrect usage and security holes. Replacing such calls does not have a high priority right now since SeqAn is usually not used on servers facing the outside world.

Preprocessor Defines Affecting SeqAn ¶

There are certain preprocessor symbols that affect the behaviour of SeqAn.

SEQAN_ENABLE_DEBUG ¶

possible value: 0, 1
default: 0
meaning: If set to 1, assertions within SeqAn (SEQAN_ASSERT...) are enabled, they are disabled otherwise. Is forced to 1 if SEQAN_ENABLE_TESTING is true. This flag will internally always correspond to the inverse of NDEBUG, i.e. setting it to 1 will force NDEBUG to be undefined and setting it to 0 will forcefully set NDEBUG.

SEQAN_ENABLE_TESTING ¶

possible value: 0, 1
default: 0
meaning: This makes the code very slow, and should only be used when running the SeqAn unit tests. Has to be set to 1 for tests to work.

SEQAN_ASYNC_IO ¶

possible value: 0, 1
default: 0 on FreeBSD/32Bit and OpenBSD/*; 1 otherwise
meaning: Whether asynchronous input/output is available.

SEQAN_HAS_EXECINFO ¶

possible value: 0, 1
default: depends on platform / existance of <execinfo.h>
meaning: This should almost always be set to 1 on non-Windows platforms!

SEQAN_HAS_BZIP2 ¶

possible value: 0, 1
default: 0
meaning: If set to 1 then libbzip2 is expected to be available. You have to link against the library (e.g. add -lbz2 to your linke rflags) and bzlib.h must be in your include path.

SEQAN_HAS_ZLIB ¶

possible value: 0, 1
default: 0
meaning: If set to 1 then zlib is expected to be available. You have to link against the library (e.g. add -lz to your linker flags) and zlib.h must be in your include path.

Settings Projects Using Seqan ¶

You normally want to have at least two build modes: one for debugging and one for optimized compiling. The following settings have to be applied to your IDE project/Makefiles (below is an example for a Makefile based project).

Debug Builds ¶

Besides enabling debug symbols and disabling optimization, there are the following SeqAn specific settings to be applied.

Add SeqAn to your include path
Define SEQAN_ENABLE_DEBUG to be 1.

This translates into the following GCC flags:

-g -O0 -DSEQAN_ENABLE_DEBUG=1 -I${PATH_TO_SEQAN_INSTALL}/include

Release/Optimized Builds ¶

Besides disabling debug symbols, enabling optimization and disabling assertions in the standard library, there are the following SeqAn specific settings to be applied.

Add SeqAn to your include path
Define NDEBUG. This will make sure that SEQAN_ENABLE_DEBUG is 0 and also other STL includes of your program are not slowed down.

This translates into the following GCC flags:

-O3 -DNDEBUG -I${PATH_TO_SEQAN_INSTALL}/include

Caution

While some guides tell you to not use -O3 this is absolutely crucial for SeqAn based applications to perform well. Unoptimized builds are slower by multiple factors!

An Example Project Based On Makefiles ¶

We will create a project with good old Makefiles and GCC. The program will not do much but can serve as a minimal example on how to use SeqAn with your own build process. You should be able to adapt this guide to your favourite build system or IDE.

The example project can be found in util/makefile_project. The project layout looks like this:

.
|-- Makefile.rules
|-- Makefile
|-- README
|-- debug
|   `-- Makefile
|-- release
|   `-- Makefile
`-- src
    `-- main.cpp

main.cpp ¶

We have one directory src for source files. The file main.cpp looks as follows:

#include <seqan/basic.h>
#include <seqan/sequence.h>
#include <seqan/stream.h>

using namespace seqan;

int main()
{
    std::cout << CharString("Hello SeqAn!") << std::endl;
    return 0;
}

It includes SeqAn headers just as you would within the SeqAn CMake framework.

Now, consider the contents of the Makefiles:

Makefile.rules ¶

Contains the necessary commands to build the object file for the program main.cpp and then make an executeable main from it and clean targets. This file is included from the files release/Makefile and debug/Makefile.

SRC=../src
CXXFLAGS+=-I../include -std=c++14

default: all
all: main

main: main.o
	$(CXX) $(LDFLAGS) -o main main.o

main.o: $(SRC)/main.cpp
	$(CXX) $(CXXFLAGS) -c -o main.o $(SRC)/main.cpp

clean:
	rm -f main.o main

.PHONY: default all clean

Makefile ¶

Allows to build both debug and release builds by calling make debug, make release or make all from the project directory. Removes all binaries with make clean.

default: all

all: debug release

debug:
	$(MAKE) -C debug

release:
	$(MAKE) -C release

clean:
	$(MAKE) -C debug clean
	$(MAKE) -C release clean

.PHONY: default all debug release clean

debug/Makefile, release/Makefile ¶

The file debug/Makefile looks as follows.

include ../Makefile.rules

CXXFLAGS+=-g -O0 -DSEQAN_ENABLE_DEBUG=1

The file release/Makefile looks as follows.

include ../Makefile.rules

CXXFLAGS+=-O3 -DNDEBUG

These Makefiles include the file Makefile.rules. They add build type specific arguments to the variables $(CXXFLAGS). For debug builds, debug symbols are enabled, optimization level 0 is chosen, testing is enabled in SeqAn and debugging is disabled. For release builds, debug symbols are not, optimization level 3 is chosen, testing and debugging are both disabled in SeqAn. For good measure, we also disable assertions in the C library with -DNDEBUG.

Notes ¶

Above we added the include path to SeqAn’s include directory manually. By changing the include path, we can install the SeqAn library anywhere. For example, we could create a directory include parallel to src, copy the release version of SeqAn into it and then change the include path of the compiler to point to this directory (value ../include).

Short Version ¶

OS	Compiler	Flags
Linux	GCC/Clang≥3.8/ICC	`-I /path/to/seqan/include -std=c++14 -O3 -DNDEBUG -W -Wall -pedantic -fopenmp -lpthread -lrt`
BSD	GCC/Clang≥3.8/ICC	`-I /path/to/seqan/include -std=c++14 -O3 -DNDEBUG -W -Wall -pedantic -fopenmp -lpthread -lexecinfo -lelf -D_GLIBCXX_USE_C99=1`
macOS	system’s Clang	`-I /path/to/seqan/include -std=c++14 -O3 -DNDEBUG -W -Wall -pedantic`
Windows	Visual Studio MSVC	`/W2 /wd4996 -D_CRT_SECURE_NO_WARNINGS`

Adapt the include path to the actual place of SeqAn’s include folder!