Build SmartPeak

Windows

STEP 1: Build OpenMS dependencies

Build OpenMS-contrib by following the OpenMS wiki instructions

Download and install the pre-compiled Boost library binaries for windows (i.e. SourceForge) and

  • The minimum required Boost version is 1.71.0

  • Ensure that these binaries are used both for OpenMS and SmartPeak

  • The only boost package required by SmartPeak is Unit Test for unit testing, however, the same version of boost must be used when compiling both OpenMS and SmartPeak

Download and install QT5 using the offline installer for windows

STEP 2: Build OpenMS

Build OpenMS following the OpenMS wiki instructions. Example cmake command on windows

cmake -DBoost_NO_SYSTEM_PATHS=ON -BOOST_INCLUDEDIR="C:/local/boost_1_73_0" -DBOOST_ROOT="C:/local/boost_1_73_0" ^
-DBOOST_LIBRARYDIR="C:/local/boost_1_73_0/lib64-msvc-14.2" -DBOOST_USE_STATIC=OFF -DWITH_GUI=OFF -DPYOPENMS=OFF ^
-DOPENMS_CONTRIB_LIBS="[OpenMS directory]/contrib/build" -DCMAKE_PREFIX_PATH="C:/qt/Qt5.12.1b/5.12.1/msvc2017_64/lib/cmake" ^
-G "Visual Studio 16 2019" -A x64 ..

  • Open “OpenMS_host” in visual studios and build only the solution for “OpenSwathAlgo” and then for “OpenMS” IN THAT ORDER

  • Add the “lib” folder in the openms-build directory to the system path variable so that the .dll’s will be found during run-time

  • or extend your current path with the following command in powershell as an elevated user:

setx path "%PATH%;[OpenMS directory]\openms-build\lib\debug;C:\qt\Qt5.12.1b\5.12.1\msvc2017_64\lib"
setx path "%PATH%;C:\local\boost_1_73_0\lib64-msvc-14.2;[SDL directory]\lib\x64"

STEP 3: Build SmartPeak dependencies

Download the latest SDL2 libraries. Add the SDL2 folder to the path environmental variable. Compile using cmake and build for “external projects” Example cmake command to download all external projects assuming that you are in the location [home directory]/smartPeak2/build_external :bash:`cmake -G "Visual Studio 16 2019" -A x64 -T host=x64 -DUSE_SUPERBUILD=ON ..` However, many of the requirements overlap with OpenMS so for practical purposes the only libraries that will need to be download are “ImGui”, “ImPlot”, and “Plog”

STEP 4: Build SmartPeak

Compile using cmake. Example cmake command on windows assuming that all external dependency libraries are in the path [home directory]/smartPeak/build_external

cmake -DEIGEN_USE_GPU=OFF -DBoost_NO_SYSTEM_PATHS=ON -BOOST_INCLUDEDIR="C:/local/boost_1_73_0/boost" -DBOOST_ROOT="C:/local/boost_1_73_0" ^
-DBOOST_LIBRARYDIR="C:/local/boost_1_73_0/lib64-msvc-14.2" -DBOOST_USE_STATIC=OFF -G "Visual Studio 16 2019" -A x64 -T host=x64 -DUSE_SUPERBUILD=OFF ^
-DEIGEN3_INCLUDE_DIR=[home directory]/smartPeak2/build_external/Dependencies/Source/eigen ^
-DPLOG_INCLUDE_DIR=[home directory]/smartPeak2/build_external/Dependencies/Source/plog/include ^
-DIMGUI_DIR=[home directory]/smartPeak2/build_external/Dependencies/Source/imgui ^
-DIMPLOT_DIR=[home directory]/smartPeak2/build_external/Dependencies/Source/implot ^
-DCMAKE_PREFIX_PATH="[OpenMS directory]/openms-build";"C:/qt/Qt5.12.1b/5.12.1/msvc2017_64/lib/cmake";"[SDL directory]/SDL"; ..

Open “SmartPeak_host” in visual studios and build the project of choice. Projects can be built using Visual Studios in the IDE by opening msbuild [build_dir]/src/SmartPeak_host and selecting the specific target to build in the SmartPeakGUI or on the command line by running e.g., msbuild [build_dir]/src/smartpeak/SmartPeak.sln /verbosity:normal /maxcpucount which will build the main SmartPeak library and then running e.g., msbuild [build_dir]/examples/SmartPeak_class_examples_smartpeak.sln -target:SmartPeakGUI /verbosity:normal /maxcpucount which will build the SmartPeak GUI.

STEP 5: Build SmartPeak-Docs

Generating the docs for SmartPeak on windows platforms is done by calling the docs build target.

In ordert to build the docs locally the following dependencies are needed:

  • Doxygen : Download and install

  • Sphinx : pip install --user sphinx

  • Breathe : pip install --user breathe

  • Exhale : pip install --user exhale

Note

Sphinx needs to be present in PATH so that the sphinx-executable can be found by CMake i.e. C:\Users\$USER\AppData\Roaming\Python\Python37\Scripts

Linux

In the below instructions it is assumed OpenMS code resides in ~/OpenMS and SmartPeak code is in ~/SmartPeak.

STEP 1: Build OpenMS dependencies

Build OpenMS-contrib by following the OpenMS wiki instructions.

Starting from Ubuntu 18.04, it’s not necessary to manually build OpenMS' contrib. The packages available in the repositories are recent enough.

STEP 2: Build OpenMS

Build OpenMS following the OpenMS wiki instructions. Example workflow:

cd ~
mkdir OpenMS-build
cd OpenMS-build
cmake -DBOOST_USE_STATIC=OFF -DHAS_XSERVER=OFF -DWITH_GUI=OFF -DENABLE_TUTORIALS=OFF -DENABLE_DOCS=OFF -DGIT_TRACKING=OFF -DENABLE_UPDATE_CHECK=OFF -DCMAKE_BUILD_TYPE=Debug -DPYOPENMS=OFF -DOPENMS_COVERAGE=OFF ~/OpenMS
make -j4 OpenMS

STEP 3: Building SmartPeak

SuperBuild helps downloading the dependencies for SmartPeak.

cd ~
mkdir SmartPeak_superbuild SmartPeak_build
cd SmartPeak_superbuild
cmake -DUSE_SUPERBUILD=ON -G "Unix Makefiles" -DCMAKE_BUILD_TYPE=Debug ~/SmartPeak
make -j4
cd ~/SmartPeak_build
cmake -DEIGEN_USE_GPU=OFF -DUSE_SUPERBUILD=OFF -DBOOST_USE_STATIC=OFF -G "Unix Makefiles" -DCMAKE_PREFIX_PATH=$HOME/OpenMS-build/ -DPLOG_INCLUDE_DIR=$HOME/SmartPeak_superbuild/Dependencies/Source/plog/include -DIMGUI_DIR=$HOME/SmartPeak_superbuild/Dependencies/Source/imgui -DIMPLOT_DIR=$HOME/SmartPeak_superbuild/Dependencies/Source/implot -DCMAKE_BUILD_TYPE=Debug ~/SmartPeak
make -j4

Some dependencies one might have to install:

sudo apt install qt5-default libeigen3-dev libxerces-c-dev coinor-libcbc-dev libsvm-dev libboost-all-dev libwildmagic-dev libsqlite3-dev libglpk-dev seqan-dev libhdf5-dev python3-pip

STEP 4: Build SmartPeak-Docs

Generating the docs for SmartPeak on Linux is done by calling the make -B docs build target.

In ordert to build the docs locally the following dependencies are needed:

  • Doxygen : sudo apt-get install -y graphviz doxygen doxygen-doc

  • Sphinx : pip install --user sphinx

  • Breathe : pip install --user breathe

  • Exhale : pip install --user exhale

macOS

Building SmartPeak and all its dependencies is as easy as on Linux. Assuming the source code for OpenMS and SmartPeak reside in the home directory i.e. ~/OpenMS ~/SmartPeak, the following steps can be taken verbatim:

STEP 1: Installing external libraries

brew is the tool of choice to get all the necessary libraries installed with ease, if it’s not present on your machines, you can install it using the following command:

/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install.sh)"

brew install cmake qt5 sdl2 boost glpk eigen sqlite hdf5 libsvm xerces-c
brew install coin-or-tools/coinor/cbc coin-or-tools/coinor/cgl coin-or-tools/coinor/clp coin-or-tools/coinor/coin_data_netlib
brew install coin-or-tools/coinor/coin_data_sample coin-or-tools/coinor/coinutils coin-or-tools/coinor/osi

STEP 2: Build OpenMS

OpemMS libs can be built wihtout GUI capabilities using the following set of commands:

cd ~
git clone --branch develop --depth 1 https://github.com/OpenMS/OpenMS.git
cd OpenMS && git submodule update --init contrib && mkdir contrib_build && cd contrib_build
cmake -DCMAKE_CXX_COMPILER=clang++ -DCMAKE_C_COMPILER=clang -DBUILD_TYPE=ALL ../contrib
cd ~/OpenMS &&  mkdir openms_debug_build && cd openms_debug_build
cmake -DCMAKE_CXX_COMPILER=clang++ -DCMAKE_C_COMPILER=clang -DCMAKE_CXX_STANDARD=14 \
-DCMAKE_CXX_EXTENSIONS=OFF -DCMAKE_PREFIX_PATH="$(brew --prefix qt5);$(brew --prefix boost);$(brew --prefix)" \
-DBOOST_USE_STATIC=OFF -DOPENMS_CONTRIB_LIBS=~/OpenMS/contrib_build/ \
-DSEQAN_INCLUDE_DIRS=~/OpenMS/contrib_build/include/seqan -DCOIN_INCLUDE_DIR=../contrib_build/include/ \
-DWM5_INCLUDE_DIR=../contrib_build/include/WildMagic/ -DWM5_Wm5Core_LIBRARY=../contrib_build/lib/libWm5Core.a \
-DWM5_Wm5Mathematics_LIBRARY=../contrib_build/lib/libWm5Mathematics.a -DHAS_XSERVER=OFF -DWITH_GUI=OFF \
-DENABLE_TUTORIALS=OFF -DENABLE_DOCS=OFF -DGIT_TRACKING=OFF -DENABLE_UPDATE_CHECK=OFF -DCMAKE_BUILD_TYPE=Debug \
-DPYOPENMS=OFF -DOPENMS_COVERAGE=OFF ..
make -j4 OpenMS

The contrib libraries are also offered by the OpenMS Team precompiled for the recent versions of clang and can be installed as follows, make sure to nagivate and fetch the contrib builds based on your macOS and Xcode versions:

cd OpenMS && mkdir contrib_build && cd contrib_build
curl -O https://abibuilder.informatik.uni-tuebingen.de/archive/openms/contrib/macOS/10.15.4/x64/appleclang-11.0.0/contrib_build.tar.gz
tar -xzf contrib_build.tar.gz
rm lib/libboost_* && rm -r include/boost && rm -r lib/cmake/Boost* && rm -r lib/cmake/boost*

STEP 3: Building SmartPeak

Building SmartPeak is done in 2 steps:

  • Fetching required libraries for SmartPeak (SuperBuild)

  • Building SmartPeak library, examples and SmartPeak GUI

This can be done using the following set of commands:

cd ~/SmartPeak && mkdir smartpeak2_debug_superbuild smartpeak2_debug_build
cd smartpeak2_debug_superbuild
cmake -DUSE_SUPERBUILD=ON -DCMAKE_BUILD_TYPE=Debug .. && make -j4

cd ../smartpeak2_debug_build
cmake -DEIGEN_USE_GPU=OFF -DUSE_SUPERBUILD=OFF -DBOOST_USE_STATIC=OFF \
-DCMAKE_PREFIX_PATH="~/OpenMS/openms_debug_build/;$(brew --prefix qt5);$(brew --prefix boost)" \
-DPLOG_INCLUDE_DIR=~/SmartPeak2/smartpeak2_debug_superbuild/Dependencies/Source/plog/include \
-DIMGUI_DIR=~/SmartPeak2/smartpeak2_debug_superbuild/Dependencies/Source/imgui \
-DIMPLOT_DIR=~/SmartPeak2/smartpeak2_debug_superbuild/Dependencies/Source/implot \
-DCMAKE_BUILD_TYPE=Debug ~/SmartPeak2
make -j4

STEP 4: Build SmartPeak-Docs

Generating the docs for SmartPeak on macOS is done by calling the make -B docs build target.

In ordert to build the docs locally the following dependencies are needed:

  • Doxygen : brew install doxygen

  • Sphinx : pip install --user sphinx

  • Breathe : pip install --user breathe

  • Exhale : pip install --user exhale