Quick Setup (using CMake)

Table of Contents

• Software
• Directory Structure
• Compiling and Running
• Adding a new source file to your project

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

Difficulty	Easy
Duration	30 Minutes
Prerequisite tutorials	No prerequisites
Recommended reading

Software

Requirements:

• gcc >= 10
• cmake >= 3.14
• git

BioC++ requires a GCC >= 10. Current versions of LLVM/Clang and VisualStudio/MSVC are not supported. You can check your GCC version by calling g++ --version. Depending on your operating system, multiple versions might be available as g++-10 or g++10. We recommend using the latest version of GCC you have access to. For more information refer to your operating system's documentation.

Directory Structure

For this project, we recommend following directory layout:

tutorial
├── source
├── build
└── biocpp-core

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

mkdir tutorial
cd tutorial
mkdir build
mkdir source
git clone https://github.com/biocpp/biocpp-core.git

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

.
├── build
├── biocpp-core
│   ├── build_system
│   ├── CHANGELOG.md
│   ├── CMakeLists.txt
│   ├── CODE_OF_CONDUCT.md
│   ├── CONTRIBUTING.md
│   ├── doc
│   ├── include
│   ├── LICENSE.md
│   ├── README.md
│   ├── submodules
│   └── 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:

#include <bio/alphabet/aminoacid/all.hpp>
#include <bio/alphabet/fmt.hpp>
 
using namespace bio::alphabet::literals;
 
int main()
{
    std::vector<bio::alphabet::aa27> protein = "HELLOWORLD"_aa27;
    fmt::print("{}\n", protein);
    return 0;
}

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

cmake_minimum_required (VERSION 3.4)
project (biocpp_core_tutorial CXX)
 
find_package (biocpp COMPONENTS core REQUIRED HINTS "${CMAKE_SOURCE_DIR}/../biocpp-core/build_system")
# OR:
#find_package (biocpp_core REQUIRED HINTS "${CMAKE_SOURCE_DIR}/../biocpp-core/build_system")
 
add_executable (hello_world hello_world.cpp)
 
target_link_libraries (hello_world biocpp::core)

The directories should now look like this:

tutorial
├── source
    ├── CMakeLists.txt
    └── hello_world.cpp
├── build
└── biocpp-core
    ├── CMakeLists.txt
    ├── LICENSE
    ...

Now we can switch to the directory build and run:

cmake ../source
make
./hello_world

The output should be Hello world.

Remarks

Depending on the standard C++ on your system, you may need to specify the compiler via -DCMAKE_CXX_COMPILER=, for example:

cmake ../source -DCMAKE_CXX_COMPILER=/path/to/executable/g++-10

Note

In some situations it can happen that the correct assembler is not found. You will see an error during the cmake configuration that says something like: ... could not understand flag m .... In this case you can try to export the Path:

export PATH=/util/bin:$PATH

and try running cmake again.

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 (biocpp-core_tutorial CXX)
 
find_package (biocpp COMPONENTS core REQUIRED HINTS "${CMAKE_SOURCE_DIR}/../biocpp-core/build_system")
 
add_executable (hello_world hello_world.cpp)
add_executable (another_program another_program.cpp)
 
target_link_libraries (hello_world biocpp::core)
target_link_libraries (another_program biocpp::core)