Software

Requirements:

gcc >= 11 or clang >= 17
cmake >= 3.16
git

Installing a Compiler

Sharg requires GCC >= 11 or LLVM/Clang >= 17. Presently, VisualStudio/MSVC is not supported. We'll offer a brief tutorial on compiler updates through common package managers and suggest some web-based alternatives. For further details, consult your OS documentation.

# Installs gcc-13

sudo add-apt-repository --no-update --yes ppa:ubuntu-toolchain-r/ppa

sudo add-apt-repository --no-update --yes ppa:ubuntu-toolchain-r/test

sudo apt-get update

sudo apt install g++-13

See https://apt.llvm.org/ if you prefer to use LLVM's Clang.
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.
brew install gcc@13

brew install llvm@17
sudo port install gcc13

sudo port install llvm-17
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.
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 Sharg in gitpod.
GitHub Codespaces offer a service similar to gitpod, including a free monthly quota. Click here to open Sharg in Codespaces. Please note that you may have to manually clone the submodules by running git submodule update --init.

Note: After installing, g++ --version should print the desired GCC version. If not, you may have to use, for example, g++-11 --version or even specify the full path to your compiler.

Similarly, you may need to install CMake and git, e.g. sudo 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
├── build
├── sharg-parser
└── source

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

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

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

.
├── build
├── sharg-parser
│   ├── CHANGELOG.md
│   ├── CMakeLists.txt
│   ├── ...
│   └── test
└── source

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:

// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
// SPDX-License-Identifier: CC0-1.0
 
#include <sharg/all.hpp>
 
int main(int argc, char ** argv)
{
    int val{};
 
    sharg::parser parser{"Eat-Me-App", argc, argv};
    parser.add_subsection("Eating Numbers");
    parser.add_option(val, sharg::config{.short_id = 'i', .long_id = "int", .description = "Desc."});
    parser.parse();
 
    return 0;
}

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

# SPDX-FileCopyrightText: 2006-2024, Knut Reinert & Freie Universität Berlin
# SPDX-FileCopyrightText: 2016-2024, Knut Reinert & MPI für molekulare Genetik
# SPDX-License-Identifier: CC0-1.0
 
cmake_minimum_required (VERSION 3.12)
project (sharg_tutorial CXX)
 
# add sharg to search path
list (APPEND CMAKE_PREFIX_PATH "${CMAKE_CURRENT_SOURCE_DIR}/../sharg-parser/cmake")
 
# require sharg with a version between >=1.0.0 and <2.0.0
find_package (sharg 1.0 REQUIRED)
 
# build app with sharg
add_executable (hello_world hello_world.cpp)
target_link_libraries (hello_world sharg::sharg)

The directories should now look like this:

.
├── build
├── sharg-parser
│   ├── CHANGELOG.md
│   ├── CMakeLists.txt
│   ├── ...
│   └── 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

This should output a basic help page. 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++-13 ../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 3.12)
project (sharg_tutorial CXX)
 
# add sharg to search path
list (APPEND CMAKE_PREFIX_PATH "${CMAKE_CURRENT_SOURCE_DIR}/../sharg-parser/cmake")
 
# require sharg with a version between >=1.0.0 and <2.0.0
find_package (sharg 1.0 REQUIRED)
 
# build app with sharg
add_executable (hello_world hello_world.cpp)
target_link_libraries (hello_world sharg::sharg)
 
add_executable (another_program another_program.cpp)
target_link_libraries (another_program sharg::sharg)

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.

Difficulty	Easy
Duration	30 Minutes
Prerequisite tutorials	No prerequisites
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