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File openms.spec of Package openms
# # spec file for package openms # # Copyright (c) 2022 SUSE LLC # # All modifications and additions to the file contributed by third parties # remain the property of their copyright owners, unless otherwise agreed # upon. The license for this file, and modifications and additions to the # file, is the same license as for the pristine package itself (unless the # license for the pristine package is not an Open Source License, in which # case the license is the MIT License). An "Open Source License" is a # license that conforms to the Open Source Definition (Version 1.9) # published by the Open Source Initiative. # Please submit bugfixes or comments via https://bugs.opensuse.org/ # # Required python-autowrap not packaged %bcond_with pyOpenMS %bcond_with documentation # GUI requires Qt build with Desktop OpenGL backend %ifarch %{arm} aarch64 %bcond_with gui %else %bcond_without gui %endif Name: openms Version: 2.8.0 Release: 0 License: BSD-3-Clause Summary: LC/MS data management and analysis suite Group: Productivity/Scientific/Chemistry URL: https://www.openms.de/ Source0: https://github.com/OpenMS/OpenMS/archive/refs/tags/Release%{version}.tar.gz # PATCH-FIX-UPSTREAM Patch0: https://patch-diff.githubusercontent.com/raw/OpenMS/OpenMS/pull/5916.patch#/fix-isnan-undeclared.patch # PATCH-FIX-UPSTREAM Patch1: https://patch-diff.githubusercontent.com/raw/OpenMS/OpenMS/pull/6302.patch#/fix-libwm5core-linkage.patch # PATCH-FIX-UPSTREAM Patch2: https://github.com/OpenMS/OpenMS/pull/5838.patch#/fix-compile-warnings.patch # PATCH-FIX-UPSTREAM Patch3: 0001-Fix-install-path-for-evergreen-headers.patch BuildRequires: chrpath BuildRequires: cmake >= 3.9 BuildRequires: desktop-file-utils BuildRequires: eigen3-devel >= 3.3.4 BuildRequires: gcc-c++ BuildRequires: glpk-devel BuildRequires: hdf5-devel BuildRequires: hicolor-icon-theme BuildRequires: libbz2-devel BuildRequires: libboost_date_time-devel BuildRequires: libboost_headers-devel BuildRequires: libboost_iostreams-devel BuildRequires: libboost_math-devel BuildRequires: libboost_regex-devel BuildRequires: libsvm-devel >= 2.91 BuildRequires: wildmagic5-devel BuildRequires: update-desktop-files BuildRequires: zlib-devel BuildRequires: pkgconfig(cbc) BuildRequires: pkgconfig(cgl) BuildRequires: pkgconfig(sqlite3) BuildRequires: pkgconfig(xerces-c) BuildRequires: cmake(Qt5Concurrent) BuildRequires: cmake(Qt5Core) BuildRequires: cmake(Qt5Network) BuildRequires: cmake(Qt5Sql) BuildRequires: cmake(Qt5Svg) BuildRequires: cmake(Qt5Test) # sqlite driver plugin required for test and at runtime BuildRequires: libqt5-sql-sqlite %if %{with gui} BuildRequires: cmake(Qt5Gui) BuildRequires: cmake(Qt5WebEngineWidgets) BuildRequires: cmake(Qt5Widgets) %endif %if %{with pyOpenMS} BuildRequires: python3-Cython BuildRequires: python3-autowrap BuildRequires: python3-numpy BuildRequires: python3-pytest BuildRequires: python3-wheel %endif %if %{with documentaton} BuildRequires: doxygen BuildRequires: graphviz BuildRequires: texlive BuildRequires: texlive-a4wide BuildRequires: texlive-xtab %endif ##Xvfb is needed to run a virtual X server used by some tests BuildRequires: xvfb-run Requires: %{name}-data = %{version} Requires: hicolor-icon-theme Requires: libqt5-sql-sqlite %description OpenMS is an open-source C++ library for LC/MS data management and analyses. It offers an infrastructure for the rapid development of mass spectrometry related software. %package tools Summary: OpenMS tools Requires: %{name}-data = %{version} %description tools Besides TOPP, OpenMS offers a range of other tools. They are not included in TOPP as they are not part of typical analysis pipelines, but they still might be very helpful to you. The UTILS tools are divided into several subgroups: - Maintenance - Signal Processing and Preprocessing - File handling - Algorithm evaluation - Peptide identification - Quantitation - Misc - Metabolite identification - Quality control %package -n python-openms Summary: OpenMS Python bindings Requires: %{name}-data = %{version} %description -n python-openms This package contains Python bindings for a large part of the OpenMS library for mass spectrometry based proteomics. It thus provides providing facile access to a feature-rich, open-source algorithm library for mass-spectrometry based proteomics analysis. These Python bindings allow raw access to the data-structures and algorithms implemented in OpenMS, specifically those for file access (mzXML, mzML, TraML, mzIdentML among others), basic signal processing (smoothing, filtering, de-isotoping and peak-picking) and complex data analysis (including label-free, SILAC, iTRAQ and SWATH analysis tools). %package devel Summary: OpenMS header files %description devel OpenMS development files. %package doc Summary: OpenMS documentation BuildArch: noarch %description doc HTML documentation and PDF tutorials of OpenMS. %package tutorials Summary: OpenMS tutorials Requires: %{name}-data = %{version} %description tutorials OpenMS executable tutorials. %package data Summary: The OpenMS data files BuildArch: noarch %description data The OpenMS data files. %prep %autosetup -n OpenMS-Release%{version} -p1 rm -rf cmake/MacOSX %build %cmake -Wno-dev \ -DBOOST_USE_STATIC=OFF \ -DENABLE_UPDATE_CHECK:BOOL=FALSE \ -DCMAKE_SKIP_RPATH:BOOL=FALSE \ -DCMAKE_SKIP_INSTALL_RPATH:BOOL=TRUE \ -DMT_ENABLE_OPENMP=ON \ -DENABLE_GCC_WERROR:BOOL=OFF \ -DENABLE_TUTORIALS:BOOL=ON \ -DENABLE_UNITYBUILD:BOOL=OFF \ -DHAS_XSERVER:BOOL=ON \ -DINSTALL_BIN_DIR:PATH=bin \ -DINSTALL_CMAKE_DIR:PATH=%{_lib}/cmake/OpenMS \ -DINSTALL_DOC_DIR:PATH=share/doc/packages/OpenMS \ -DINSTALL_INCLUDE_DIR:PATH=include \ -DINSTALL_LIB_DIR:PATH=%{_lib} \ -DINSTALL_SHARE_DIR:PATH=share/OpenMS \ -DPACKAGE_TYPE:STRING=none \ -DWITH_GUI:BOOL=%{?with_gui:ON}%{!?with_gui:OFF} \ %if 0%{?with_pyOpenMS} -DPYOPENMS=ON \ %else -DPYOPENMS=OFF \ %endif %{nil} %cmake_build all %if 0%{?with_pyOpenMS} %cmake_build pyopenms %endif %cmake_build doc %install %cmake_install %if 0%{?with_pyOpenMS} ## pyOpenMS installation pushd pyOpenMS python3 setup.py install --skip-build --root %{buildroot} ## Fix standard permissions chmod 0755 %{buildroot}%{python_sitearch}/pyopenms/pyopenms.so popd %endif %if %{with gui} ## Install icons install -m 0644 -D -t %{buildroot}%{_datadir}/icons/hicolor/64x64/apps src/openms_gui/source/VISUAL/ICONS/TOPPAS.png install -m 0644 -D -t %{buildroot}%{_datadir}/icons/hicolor/64x64/apps src/openms_gui/source/VISUAL/ICONS/TOPPView.png install -m 0644 -D -t %{buildroot}%{_datadir}/icons/hicolor/64x64/apps src/openms_gui/source/VISUAL/ICONS/INIFileEditor.png ## Move files to correct location mkdir -p %{buildroot}%{_datadir}/applications mv %{buildroot}%{_datadir}/OpenMS/DESKTOP/*.desktop %{buildroot}%{_datadir}/applications sed -i -e 's@Icon=.*@Icon=TOPPAS@' %{buildroot}%{_datadir}/applications/TOPPAS.desktop sed -i -e 's@Icon=.*@Icon=TOPPView@' %{buildroot}%{_datadir}/applications/TOPPView.desktop mkdir -p %{buildroot}%{_datadir}/metainfo/ mv %{buildroot}%{_datadir}/OpenMS/DESKTOP/TOPPView.appdata.xml %{buildroot}%{_datadir}/metainfo/ mv %{buildroot}%{_datadir}/OpenMS/DESKTOP/TOPPAS.appdata.xml %{buildroot}%{_datadir}/metainfo/ rm %{buildroot}%{_datadir}/OpenMS/DESKTOP/readme.txt rmdir %{buildroot}%{_datadir}/OpenMS/DESKTOP ## Create inifileeditor .desktop file %suse_update_desktop_file -c INIFileEditor INIFileEditor INIFileEditor INIFileEditor INIFileEditor %else rm -Rf %{buildroot}%{_datadir}/OpenMS/DESKTOP %endif ##Install Tutorials executable mkdir -p %{buildroot}%{_bindir} cp -a %{__builddir}/bin/Tutorial_* %{buildroot}%{_bindir} chrpath -d %{buildroot}%{_bindir}/Tutorial_* %post -p /sbin/ldconfig %postun -p /sbin/ldconfig %check ## Make all test export PATH=$PWD/%{__builddir}/bin:$PATH export OPENMS_DATA_PATH=$PWD/share/OpenMS:$OPENMS_DATA_PATH pushd %{__builddir} ## Run a Virtual X server waiting 3 seconds before # TOPP_DatabaseSuitability_* depends on Comet (https://github.com/UWPR/Comet) # Some tests known to fail, see https://github.com/OpenMS/OpenMS/issues/5541: # - PrecursorIonSelectionPreprocessing_test # - DetectabilitySimulation_test # - MRMAssay_test # - MRMFeatureSelector_test # - TOPP_OpenPepXL_1_out_2 # - TOPP_OpenPepXLLF_1_out_2 # Numeric problems on ix86 %ifnarch %{ix86} xvfb-run -a ctest --output-on-failure --force-new-ctest-process %{?_smp_mflags} \ --exclude-regex 'TOPP_DatabaseSuitability_.*|PrecursorIonSelectionPreprocessing_test|DetectabilitySimulation_test|MRMAssay_test|MRMFeatureSelector_test|TOPP_OpenPepXL.*_1_out_2' popd %endif ##pyOpenMS tests including mem leak #%%if 0%{?with_pyOpenMS} #cd pyOpenMS ## See https://github.com/OpenMS/OpenMS/issues/1389 #python ./run_memleaks.py #python ./run_nose.py #%%endif %files %doc CHANGELOG AUTHORS README.md %license License.txt %if %{with gui} %{_bindir}/TOPPView %{_bindir}/TOPPAS %{_bindir}/INIFileEditor %{_bindir}/Resampler %{_bindir}/ExecutePipeline %{_bindir}/SwathWizard %{_datadir}/applications/TOPPAS.desktop %{_datadir}/applications/TOPPView.desktop %{_datadir}/applications/INIFileEditor.desktop %dir %{_datadir}/metainfo/ %{_datadir}/metainfo/TOPPView.appdata.xml %{_datadir}/metainfo/TOPPAS.appdata.xml %{_datadir}/icons/hicolor/64x64/apps/*png %endif %{_bindir}/DTAExtractor %{_bindir}/FileConverter %{_bindir}/FileInfo %{_bindir}/FileMerger %{_bindir}/IDMerger %{_bindir}/IDRipper %{_bindir}/IDFileConverter %{_bindir}/MapStatistics %{_bindir}/SpectraMerger %{_bindir}/TextExporter %{_bindir}/MzTabExporter %{_bindir}/BaselineFilter %{_bindir}/InternalCalibration %{_bindir}/MapNormalizer %{_bindir}/MassTraceExtractor %{_bindir}/NoiseFilterGaussian %{_bindir}/NoiseFilterSGolay %{_bindir}/PeakPickerHiRes %{_bindir}/PeakPickerWavelet %{_bindir}/PrecursorMassCorrector %{_bindir}/HighResPrecursorMassCorrector %{_bindir}/SpectraFilterBernNorm %{_bindir}/SpectraFilterMarkerMower %{_bindir}/SpectraFilterNLargest %{_bindir}/SpectraFilterNormalizer %{_bindir}/SpectraFilterParentPeakMower %{_bindir}/SpectraFilterScaler %{_bindir}/SpectraFilterSqrtMower %{_bindir}/SpectraFilterThresholdMower %{_bindir}/SpectraFilterWindowMower %{_bindir}/TOFCalibration %{_bindir}/Decharger %{_bindir}/EICExtractor %{_bindir}/FeatureFinderCentroided %{_bindir}/FeatureFinderIsotopeWavelet %{_bindir}/FeatureFinderMetabo %{_bindir}/FeatureFinderMRM %{_bindir}/IsobaricAnalyzer %{_bindir}/ProteinQuantifier %{_bindir}/ProteinResolver %{_bindir}/SeedListGenerator %{_bindir}/ConsensusMapNormalizer %{_bindir}/MapAlignerIdentification %{_bindir}/MapAlignerPoseClustering %{_bindir}/MapAlignerSpectrum %{_bindir}/MapRTTransformer %{_bindir}/FeatureLinkerLabeled %{_bindir}/FeatureLinkerUnlabeled %{_bindir}/FeatureLinkerUnlabeledQT %{_bindir}/CompNovo %{_bindir}/CompNovoCID %{_bindir}/MascotAdapter %{_bindir}/MascotAdapterOnline %{_bindir}/MyriMatchAdapter %{_bindir}/OMSSAAdapter %{_bindir}/PepNovoAdapter %{_bindir}/XTandemAdapter %{_bindir}/SpecLibSearcher %{_bindir}/ConsensusID %{_bindir}/FalseDiscoveryRate %{_bindir}/IDConflictResolver %{_bindir}/IDFilter %{_bindir}/IDMapper %{_bindir}/IDPosteriorErrorProbability %{_bindir}/IDRTCalibration %{_bindir}/IDScoreSwitcher %{_bindir}/PeptideIndexer %{_bindir}/ProteinInference %{_bindir}/InclusionExclusionListCreator %{_bindir}/PrecursorIonSelector %{_bindir}/LuciphorAdapter %{_bindir}/MetaProSIP %{_bindir}/MRMMapper %{_bindir}/MzMLSplitter %{_bindir}/OpenSwathAssayGenerator %{_bindir}/OpenSwathDecoyGenerator %{_bindir}/OpenSwathChromatogramExtractor %{_bindir}/OpenSwathAnalyzer %{_bindir}/OpenSwathRTNormalizer %{_bindir}/OpenSwathFeatureXMLToTSV %{_bindir}/OpenSwathConfidenceScoring %{_bindir}/PTModel %{_bindir}/PTPredict %{_bindir}/RTModel %{_bindir}/RTPredict %{_bindir}/GenericWrapper %{_bindir}/FeatureFinderIdentification %{_bindir}/FeatureFinderMultiplex %{_bindir}/FidoAdapter %{_bindir}/MRMTransitionGroupPicker %{_bindir}/MSGFPlusAdapter %{_bindir}/MetaboliteSpectralMatcher %{_bindir}/OpenSwathWorkflow %{_bindir}/PeakPickerIterative %{_bindir}/SimpleSearchEngine %{_bindir}/AssayGeneratorMetabo %{_bindir}/ClusterMassTraces %{_bindir}/ClusterMassTracesByPrecursor %{_bindir}/CometAdapter %{_bindir}/CruxAdapter %{_bindir}/DatabaseFilter %{_bindir}/DatabaseSuitability %{_bindir}/Epifany %{_bindir}/ExternalCalibration %{_bindir}/FeatureFinderMetaboIdent %{_bindir}/FeatureLinkerUnlabeledKD %{_bindir}/GNPSExport %{_bindir}/MSFraggerAdapter %{_bindir}/MSstatsConverter %{_bindir}/MaRaClusterAdapter %{_bindir}/MapAlignerTreeGuided %{_bindir}/MetaboliteAdductDecharger %{_bindir}/MultiplexResolver %{_bindir}/NovorAdapter %{_bindir}/NucleicAcidSearchEngine %{_bindir}/OpenMSDatabasesInfo %{_bindir}/OpenPepXL %{_bindir}/OpenPepXLLF %{_bindir}/OpenSwathFileSplitter %{_bindir}/PSMFeatureExtractor %{_bindir}/PercolatorAdapter %{_bindir}/ProteomicsLFQ %{_bindir}/QualityControl %{_bindir}/RNADigestor %{_bindir}/RNAMassCalculator %{_bindir}/RNPxlSearch %{_bindir}/SiriusAdapter %{_bindir}/SpectraSTSearchAdapter %{_bindir}/StaticModification %{_bindir}/TICCalculator %{_bindir}/TargetedFileConverter %{_bindir}/TriqlerConverter %{_bindir}/XFDR %{_libdir}/lib*.so %files tools %if %{with gui} %{_bindir}/INIUpdater %{_bindir}/ImageCreator %endif %{_bindir}/FileFilter %{_bindir}/IDDecoyProbability %{_bindir}/OpenMSInfo %{_bindir}/PhosphoScoring %{_bindir}/RNPxlXICFilter %{_bindir}/FuzzyDiff %{_bindir}/XMLValidator %{_bindir}/SemanticValidator %{_bindir}/CVInspector %{_bindir}/IDSplitter %{_bindir}/OpenSwathMzMLFileCacher %{_bindir}/FFEval %{_bindir}/LabeledEval %{_bindir}/RTEvaluation %{_bindir}/TransformationEvaluation %{_bindir}/Digestor %{_bindir}/DigestorMotif %{_bindir}/DecoyDatabase %{_bindir}/SequenceCoverageCalculator %{_bindir}/IDExtractor %{_bindir}/IDMassAccuracy %{_bindir}/SpecLibCreator %{_bindir}/ERPairFinder %{_bindir}/MRMPairFinder %{_bindir}/MassCalculator %{_bindir}/MSSimulator %{_bindir}/SvmTheoreticalSpectrumGeneratorTrainer %{_bindir}/DeMeanderize %{_bindir}/OpenSwathDIAPreScoring %{_bindir}/OpenSwathRewriteToFeatureXML %{_bindir}/AccurateMassSearch %{_bindir}/QCCalculator %{_bindir}/QCImporter %{_bindir}/QCEmbedder %{_bindir}/QCExporter %{_bindir}/QCExtractor %{_bindir}/QCMerger %{_bindir}/QCShrinker %files data %{_datadir}/OpenMS/ %exclude %{_datadir}/OpenMS/examples %files tutorials %{_bindir}/Tutorial_* %{_datadir}/OpenMS/examples %files devel %{_includedir}/OpenMS/ %dir %{_libdir}/cmake %{_libdir}/cmake/OpenMS %if %{with documentation} %files doc %{_datadir}/doc/OpenMS/ %endif %if %{with pyOpenMS} %files -n python-openms %license src/pyOpenMS/License.txt %{python_sitearch}/pyopenms/ %{python_sitearch}/pyopenms-*.egg-info/ %endif %changelog
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