## START: Set by rpmautospec ## (rpmautospec version 0.3.5) ## RPMAUTOSPEC: autorelease, autochangelog %define autorelease(e:s:pb:n) %{?-p:0.}%{lua: release_number = 4; base_release_number = tonumber(rpm.expand("%{?-b*}%{!?-b:1}")); print(release_number + base_release_number - 1); }%{?-e:.%{-e*}}%{?-s:.%{-s*}}%{!?-n:%{?dist}} ## END: Set by rpmautospec %bcond_without check %bcond_with debug ExclusiveArch: %{qt5_qtwebengine_arches} # LTO flags break Python binding on i686 %define _lto_cflags %{nil} # Python binding %global with_pyOpenMS 1 Obsoletes: python3-openms < 0:2.7.0-2 Obsoletes: python2-openms < 0:2.4.0-1 # # Filter private libraries %global __provides_exclude ^(%%(find %{buildroot}%{_libdir}/OpenMS -name '*.so' | xargs -n1 basename | sort -u | paste -s -d '|' -)) %global __requires_exclude ^(%%(find %{buildroot}%{_libdir}/OpenMS -name '*.so' | xargs -n1 basename | sort -u | paste -s -d '|' -)) Name: openms Summary: LC/MS data management and analyses Version: 3.1.0 Epoch: 1 Release: %autorelease -p -e pre1 License: BSD URL: http://www.openms.de/ Source0: https://github.com/OpenMS/OpenMS/archive/Release%{version}/OpenMS-Release%{version}.tar.gz ##TOPPView, TOPPAS, INIFileEditor .desktop and icon files Source1: https://raw.githubusercontent.com/OpenMS/OpenMS/develop/src/openms_gui/source/VISUAL/ICONS/TOPPView.png Source2: https://raw.githubusercontent.com/OpenMS/OpenMS/develop/src/openms_gui/source/VISUAL/ICONS/TOPPAS.png Source3: https://raw.githubusercontent.com/OpenMS/OpenMS/develop/src/openms_gui/source/VISUAL/ICONS/INIFileEditor.png Source4: inifileeditor.desktop BuildRequires: make BuildRequires: cmake BuildRequires: patchelf BuildRequires: coin-or-Cbc-devel BuildRequires: coin-or-Cgl-devel BuildRequires: coin-or-Clp-devel BuildRequires: coin-or-CoinUtils-devel BuildRequires: coin-or-Osi-devel BuildRequires: hdf5-devel BuildRequires: libsvm-devel BuildRequires: gcc-c++ BuildRequires: gsl-devel BuildRequires: glpk-devel BuildRequires: qt5-qtbase-devel BuildRequires: qt5-qtx11extras-devel BuildRequires: qt5-qtwebkit-devel BuildRequires: qt5-qtsvg-devel BuildRequires: qt5-qtwebengine-devel BuildRequires: xerces-c-devel BuildRequires: boost-devel BuildRequires: sqlite-devel BuildRequires: wildmagic5-devel BuildRequires: zlib-devel BuildRequires: bzip2-devel BuildRequires: tbb-devel BuildRequires: eigen3-devel BuildRequires: desktop-file-utils BuildRequires: percolator BuildRequires: libappstream-glib Requires: qt5-qtdeclarative-devel%{?_isa} ## Build documentation ## Doxygen useful only on SVN versions BuildRequires: doxygen, dos2unix, graphviz BuildRequires: texlive, texlive-a4wide, texlive-xtab ##Xvfb is needed to run a virtual X server used by some tests BuildRequires: xorg-x11-server-Xvfb, gnuplot, gawk Requires: percolator%{?_isa} Requires: %{name}-data%{?_isa} = 1:%{version}-%{release} Requires: R-core%{?_isa} # Remove -O0 flag for tests compiling Patch0: %{name}-remove_testflag.patch %description OpenMS is a C++ library for LC-MS data management and analyses. It offers an infrastructure for the rapid development of mass spectrometry related software. OpenMS is free software available under the three clause BSD license and runs under Windows, MacOSX and Linux. It comes with a vast variety of pre-built and ready-to-use tools for proteomics and metabolomics data analysis (TOPPTools) and powerful 2D and 3D visualization(TOPPView). OpenMS offers analyses for various quantitation protocols, including label-free quantitation, SILAC, iTRAQ, SRM, SWATH, etc. It provides built-in algorithms for de-novo identification and database search, as well as adapters to other state-of-the art tools like XTandem, Mascot, OMSSA, etc. It supports easy integration of OpenMS built tools into workflow engines like Knime, Galaxy, WS-Pgrade, and TOPPAS via the TOPPtools concept and a unified parameter handling via a 'common tool description' (CTD) scheme. The OpenMS Proteomics Pipeline is a pipeline for the analysis of HPLC-MS data. It consists of several small applications that can be chained to create analysis pipelines tailored for a specific problem. The TOPP tools are divided into several subgroups: - Graphical Tools - File Handling - Signal Processing and Preprocessing - Quantitation - Map Alignment - Protein/Peptide Identification - Protein/Peptide Processing - Targeted Experiments - Peptide Property Prediction - Misc %package utilities Summary: OpenMS utilities Requires: %{name}-data%{?_isa} = 1:%{version}-%{release} Obsoletes: %{name}-tools < 1:3.1.0-1 %description utilities Besides TOPP, OpenMS offers a range of utilities. 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 Utilities are divided into several subgroups: - Maintenance - Signal Processing and Preprocessing - File handling - Algorithm evaluation - Peptide identification - Quantitation - Misc - Metabolite identification - Quality control %if 0%{?with_pyOpenMS} %package -n python3-openms Summary: Python wrapper for OpenMS %py_provides python3-%{name} BuildRequires: python3-setuptools BuildRequires: python3-devel BuildRequires: python3-numpy BuildRequires: python3-nose BuildRequires: python3-autowrap >= 0.8.1 BuildRequires: python3-pip BuildRequires: %{_bindir}/cython BuildRequires: python3-wheel BuildRequires: python3-biopython BuildRequires: python3-virtualenv BuildRequires: python3-pandas BuildRequires: python3-pytest Requires: python3-biopython Requires: %{name}%{?_isa} = 1:%{version}-%{release} %description -n python3-openms This package contains Python3 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). %endif %package devel Summary: OpenMS header files Requires: %{name}%{?_isa} = 1:%{version}-%{release} %description devel OpenMS development files. %package data Summary: The OpenMS data files %description data The OpenMS data files. %package doc Summary: OpenMS documentation %description doc HTML documentation of OpenMS. %prep %autosetup -N -n OpenMS-Release%{version} %patch -P 0 -p1 -b .backup # Remove invalid tags sed -e 's| ||g' -i share/OpenMS/DESKTOP/*.appdata.xml %build # Likely running out of memory during build %global _smp_ncpus_max 2 mkdir -p build %if %{with debug} cmake -Wno-dev -B build -S ./ -DCMAKE_CXX_COMPILER_VERSION:STRING=$(gcc -dumpversion) \ -DENABLE_UPDATE_CHECK:BOOL=OFF \ -DCMAKE_COLOR_MAKEFILE:BOOL=ON \ -DENABLE_IPO:BOOL=ON \ -DCMAKE_CXX_FLAGS_DEBUG:STRING="-DDEBUG -O0 -g %{__global_ldflags}" -DCMAKE_C_FLAGS_DEBUG:STRING="-DDEBUG -O0 -g %{__global_ldflags}" \ -DCMAKE_BUILD_TYPE=Debug \ -DBoost_IOSTREAMS_LIBRARY_DEBUG:FILEPATH=%{_libdir}/libboost_iostreams.so \ -DBoost_MATH_C99_LIBRARY_DEBUG:FILEPATH=%{_libdir}/libboost_math_c99.so \ -DBoost_REGEX_LIBRARY_DEBUG:FILEPATH=%{_libdir}/libboost_regex.so \ -DXercesC_LIBRARY_DEBUG:FILEPATH=%{_libdir}/libxerces-c.so \ %else %cmake -Wno-dev -B build -S ./ -DCMAKE_CXX_COMPILER_VERSION:STRING=$(gcc -dumpversion) \ -DGIT_TRACKING:BOOL=OFF \ -DENABLE_UPDATE_CHECK:BOOL=OFF \ -DCMAKE_COLOR_MAKEFILE:BOOL=ON \ -DCMAKE_CXX_FLAGS_RELEASE:STRING="-Wno-cpp %{build_cxxflags}" -DCMAKE_C_FLAGS_RELEASE:STRING="-Wno-cpp %{build_cflags}" \ -DCMAKE_BUILD_TYPE=Release \ -DBoost_IOSTREAMS_LIBRARY_RELEASE:FILEPATH=%{_libdir}/libboost_iostreams.so \ -DBoost_MATH_C99_LIBRARY_RELEASE:FILEPATH=%{_libdir}/libboost_math_c99.so \ -DBoost_REGEX_LIBRARY_RELEASE:FILEPATH=%{_libdir}/libboost_regex.so \ -DXercesC_LIBRARY_RELEASE:FILEPATH=%{_libdir}/libxerces-c.so \ %endif -DCMAKE_VERBOSE_MAKEFILE=TRUE -DCMAKE_PREFIX_PATH=%{_prefix} \ -DENABLE_SVN=OFF -DBOOST_USE_STATIC=OFF \ -DCMAKE_SKIP_RPATH:BOOL=NO -DCMAKE_SKIP_INSTALL_RPATH:BOOL=NO \ -DMT_ENABLE_OPENMP=ON -DENABLE_GCC_WERROR:BOOL=OFF \ -DPERCOLATOR_BINARY:FILEPATH=%{_bindir}/percolator \ -DBOOST_USE_STATIC:BOOL=OFF -DBoost_INCLUDE_DIR:PATH=%{_includedir} \ -DENABLE_TUTORIALS:BOOL=OFF -DENABLE_UNITYBUILD:BOOL=OFF \ -DHAS_XSERVER:BOOL=OFF \ -DCMAKE_INSTALL_PREFIX=%{_prefix} \ -DINSTALL_BIN_DIR:PATH=bin -DINSTALL_CMAKE_DIR:PATH=%{_lib}/cmake/OpenMS \ -DINSTALL_DOC_DIR:PATH=share/doc/openms-doc -DINSTALL_INCLUDE_DIR:PATH=include \ -DINSTALL_LIB_DIR:PATH=%{_lib}/OpenMS -DINSTALL_SHARE_DIR:PATH=share/OpenMS \ -DPACKAGE_TYPE:STRING=none -DWITH_GUI:BOOL=ON \ -DXercesC_INCLUDE_DIRS:PATH=%{_includedir}/xercesc \ -DOPENMS_DISABLE_UPDATE_CHECK:BOOL=OFF -DENABLE_UPDATE_CHECK:BOOL=OFF -DGIT_TRACKING:BOOL=OFF \ %if %{?__isa_bits:%{__isa_bits}}%{!?__isa_bits:32} == 64 -DOPENMS_64BIT_ARCHITECTURE:BOOL=ON \ %else -DOPENMS_64BIT_ARCHITECTURE:BOOL=OFF \ %endif %if %{with check} -DBUILD_TESTING:BOOL=ON \ -DBUILD_EXAMPLES:BOOL=ON \ -DENABLE_TOPP_TESTING:BOOL=ON \ -DENABLE_CLASS_TESTING:BOOL=ON \ %else -DBUILD_TESTING:BOOL=OFF \ -DBUILD_EXAMPLES:BOOL=OFF \ -DENABLE_TOPP_TESTING:BOOL=OFF \ -DENABLE_CLASS_TESTING:BOOL=OFF \ %endif %if 0%{?with_pyOpenMS} -DPYOPENMS=ON -DPYTHON_EXECUTABLE:FILEPATH=%{__python3} \ -DCYTHON_EXECUTABLE:FILEPATH=%{_bindir}/cython3 \ -DPY_NUM_THREADS:STRING=2 -DPY_NUM_MODULES:STRING=4 %else -DPYOPENMS=OFF %endif %if %{with check} %make_build all -C build %else %make_build OpenMS TOPP GUI -C build %endif %if 0%{?with_pyOpenMS} export LD_LIBRARY_PATH=$PWD/lib:$LD_LIBRARY_PATH make -j1 pyopenms -C build %endif %install export LD_LIBRARY_PATH=$PWD/lib:$LD_LIBRARY_PATH %{_bindir}/xvfb-run -a %make_install -C build # RHBZ#2231587 ln -sfv %{_libdir}/libQt5QuickWidgets.so %{buildroot}%{_libdir}/OpenMS/libQt5QuickWidgets.so.%(pkg-config --modversion Qt5WebEngine) ln -sfv %{_libdir}/libQt5QuickWidgets.so %{buildroot}%{_libdir}/OpenMS/libQt5QuickWidgets.so.5 # Install executable tests %if %{with check} install -pm 755 build/src/tests/class_tests/bin/*_test %{buildroot}%{_bindir}/ %endif # Fix rpaths patchelf --set-rpath %{_libdir}/OpenMS %{buildroot}%{_bindir}/* patchelf --set-rpath %{_libdir}/OpenMS %{buildroot}%{_libdir}/OpenMS/*.so %if 0%{?with_pyOpenMS} pushd build/pyOpenMS %py3_install ln -s -f %{_libdir}/OpenMS/libOpenMS.so %{buildroot}%{python3_sitearch}/pyopenms/libOpenMS.so ln -s -f %{_libdir}/OpenMS/libOpenSwathAlgo.so %{buildroot}%{python3_sitearch}/pyopenms/libOpenSwathAlgo.so ln -s -f %{_libdir}/OpenMS/libSuperHirn.so %{buildroot}%{python3_sitearch}/pyopenms/libSuperHirn.so ## Fix R script sed -i "1 s|^#!/usr/bin/env Rscript\b|#!/usr/bin/Rscript|" %{buildroot}%{python3_sitearch}/pyopenms/share/OpenMS/SCRIPTS/plot_trafo.R chmod 0755 %{buildroot}%{python3_sitearch}/pyopenms/share/OpenMS/SCRIPTS/plot_trafo.R sed -i -e '1i#!/usr/bin/Rscript' %{buildroot}%{python3_sitearch}/pyopenms/share/OpenMS/SCRIPTS/mzTab2tsv_PEP.R sed -i -e '1i#!/usr/bin/Rscript' %{buildroot}%{python3_sitearch}/pyopenms/share/OpenMS/SCRIPTS/mzTab2tsv_PRT.R sed -i -e '1i#!/usr/bin/Rscript' %{buildroot}%{python3_sitearch}/pyopenms/share/OpenMS/SCRIPTS/mzTab2tsv_PSM.R # wrong-script-end-of-line-encoding sed -i 's/\r$//' %{buildroot}%{python3_sitearch}/pyopenms/share/OpenMS/SCRIPTS/mzTab2tsv_PRT.R sed -i 's/\r$//' %{buildroot}%{python3_sitearch}/pyopenms/share/OpenMS/TOOLS/EXTERNAL/Rscript_mzTab2tsv_PRT.ttd sed -i 's/\r$//' %{buildroot}%{python3_sitearch}/pyopenms/share/OpenMS/TOOLS/EXTERNAL/Rscript_mzTab2tsv_PSM.ttd # OBO should be a text file format used by OBO-Edit chmod 0644 %{buildroot}%{python3_sitearch}/pyopenms/share/OpenMS/CV/*.obo chmod 0644 %{buildroot}%{python3_sitearch}/pyopenms/share/OpenMS/TOOLS/EXTERNAL/*.ttd chmod 0644 %{buildroot}%{python3_sitearch}/pyopenms/share/OpenMS/CHEMISTRY/Enzymes.xml popd %endif # with_pyOpenMS ##Install TOPPAS/TOPPView .png icons mkdir -p %{buildroot}%{_datadir}/icons/TOPP/pixmaps install -pm 644 %{SOURCE1} %{buildroot}%{_datadir}/icons/TOPP install -pm 644 %{SOURCE2} %{buildroot}%{_datadir}/icons/TOPP install -pm 644 %{SOURCE3} %{buildroot}%{_datadir}/icons/TOPP ##Install TOPPAS/TOPPView/inifileeditor .desktop files mkdir -p %{buildroot}%{_datadir}/applications desktop-file-install \ --set-key=Exec --set-value="env OPENMS_DATA_PATH=%{_datadir}/OpenMS TOPPAS" \ --set-icon=%{_datadir}/icons/TOPP/TOPPAS.png \ --set-key=StartupNotify --set-value=true \ --add-category=Utility \ --dir=%{buildroot}%{_datadir}/applications share/OpenMS/DESKTOP/TOPPAS.desktop desktop-file-install \ --set-key=Exec --set-value="env OPENMS_DATA_PATH=%{_datadir}/OpenMS TOPPView %U" \ --set-icon=%{_datadir}/icons/TOPP/TOPPView.png \ --set-key=StartupNotify --set-value=true \ --add-category=Utility \ --dir=%{buildroot}%{_datadir}/applications share/OpenMS/DESKTOP/TOPPView.desktop desktop-file-install \ --add-category=Utility \ --set-key=Exec --set-value="env OPENMS_DATA_PATH=%{_datadir}/OpenMS INIFileEditor" \ --dir=%{buildroot}%{_datadir}/applications %{SOURCE4} ##Install appdata files mkdir -p %{buildroot}%{_metainfodir} install -pm 644 share/OpenMS/DESKTOP/*.appdata.xml %{buildroot}%{_metainfodir}/ ##HTML files copied ##I want to pack them by using %%doc macro cp -a %{buildroot}%{_datadir}/doc/openms-doc/html html rm -rf %{buildroot}%{_datadir}/doc/openms-doc/html ## Fix R script sed -i "1 s|^#!/usr/bin/env Rscript\b|#!/usr/bin/Rscript|" %{buildroot}%{_datadir}/OpenMS/SCRIPTS/plot_trafo.R chmod 0755 %{buildroot}%{_datadir}/OpenMS/SCRIPTS/plot_trafo.R # Remove unused files rm -rf %{buildroot}%{_includedir}/thirdparty %if %{with check} cp -a %{buildroot}%{_datadir}/OpenMS/examples/examples/* %{buildroot}%{_datadir}/OpenMS/examples/ rm -rf %{buildroot}%{_datadir}/OpenMS/examples/examples %endif %check appstream-util validate-relax --nonet %{buildroot}%{_metainfodir}/*.appdata.xml desktop-file-validate %{buildroot}%{_datadir}/applications/*.desktop %if %{with check} ## starting tests export LD_LIBRARY_PATH=%{buildroot}%{_libdir}/OpenMS export PATH=%{buildroot}%{_bindir}:%{_bindir} export OPENMS_DATA_PATH=%{buildroot}%{_datadir}/OpenMS export PYTHONPATH=%{buildroot}%{python3_sitearch}:../src/OpenMS LD_PRELOAD=%{buildroot}%{_libdir}/OpenMS/libOpenMS_GUI.so LD_PRELOAD=%{buildroot}%{_libdir}/OpenMS/libOpenMS.so LD_PRELOAD=%{buildroot}%{_libdir}/OpenMS/libOpenSwathAlgo.so LD_PRELOAD=%{buildroot}%{_libdir}/OpenMS/libSuperHirn.so # FAILED: 'ratio of numbers is too large' for some tests ctest -j 1 -VV --force-new-ctest-process --output-on-failure --test-dir build -E 'MRMAssay_test|SVMWrapper_test|File_test|TOPP_OpenSwathWorkflow|MRMTransitionGroupPicker_test|Deisotoper_test|IsobaricAnalyzer' %endif %files %{_bindir}/TOPPView %{_bindir}/TOPPAS %{_bindir}/INIFileEditor %{_bindir}/DTAExtractor %{_bindir}/DatabaseSuitability %{_bindir}/StaticModification %{_bindir}/SwathWizard %{_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}/Resampler %{_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}/FeatureLinkerUnlabeledKD %{_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}/MascotAdapter %{_bindir}/MascotAdapterOnline %{_bindir}/XTandemAdapter %{_bindir}/SpecLibSearcher %{_bindir}/ConsensusID %{_bindir}/FalseDiscoveryRate %{_bindir}/IDConflictResolver %{_bindir}/IDFilter %{_bindir}/IDMapper %{_bindir}/IDPosteriorErrorProbability %{_bindir}/IDRTCalibration %{_bindir}/PeptideIndexer %{_bindir}/ProteinInference %{_bindir}/MRMMapper %{_bindir}/MetaProSIP %{_bindir}/OpenSwathDecoyGenerator %{_bindir}/OpenSwathChromatogramExtractor %{_bindir}/OpenSwathAnalyzer %{_bindir}/OpenSwathRTNormalizer %{_bindir}/OpenSwathFeatureXMLToTSV %{_bindir}/OpenSwathConfidenceScoring %{_bindir}/OpenSwathAssayGenerator %{_bindir}/GenericWrapper %{_bindir}/ExecutePipeline %{_bindir}/FeatureFinderIdentification %{_bindir}/FeatureFinderMultiplex %{_bindir}/MRMTransitionGroupPicker %{_bindir}/MSGFPlusAdapter %{_bindir}/MetaboliteSpectralMatcher %{_bindir}/OpenSwathWorkflow %{_bindir}/PeakPickerIterative %{_bindir}/PercolatorAdapter %{_bindir}/SimpleSearchEngine %{_bindir}/IDScoreSwitcher %{_bindir}/MzMLSplitter %{_bindir}/LuciphorAdapter %{_bindir}/SageAdapter %{_bindir}/DatabaseFilter %{_bindir}/RNPxlSearch %{_metainfodir}/*.appdata.xml %{_datadir}/applications/TOPPAS.desktop %{_datadir}/applications/TOPPView.desktop %{_datadir}/applications/inifileeditor.desktop %{_datadir}/icons/TOPP/ %{_libdir}/OpenMS/ %dir %{_libdir}/cmake/OpenMS %{_libdir}/cmake/OpenMS/OpenMSConfig.cmake %{_libdir}/cmake/OpenMS/OpenMSConfigVersion.cmake %files utilities %{_bindir}/AssayGeneratorMetabo %{_bindir}/ClusterMassTraces %{_bindir}/ClusterMassTracesByPrecursor %{_bindir}/Epifany %{_bindir}/FeatureFinderMetaboIdent %{_bindir}/GNPSExport %{_bindir}/NucleicAcidSearchEngine %{_bindir}/ProteomicsLFQ %{_bindir}/QualityControl %{_bindir}/RNAMassCalculator %{_bindir}/MapAlignerTreeGuided %{_bindir}/MSFraggerAdapter %{_bindir}/MSstatsConverter %{_bindir}/MaRaClusterAdapter %{_bindir}/NovorAdapter %{_bindir}/RNADigestor %{_bindir}/CometAdapter %{_bindir}/MetaboliteAdductDecharger %{_bindir}/OpenPepXL %{_bindir}/OpenPepXLLF %{_bindir}/OpenMSDatabasesInfo %{_bindir}/PSMFeatureExtractor %{_bindir}/SiriusAdapter %{_bindir}/XFDR %{_bindir}/RNPxlSearch %{_bindir}/SpectraSTSearchAdapter %{_bindir}/DatabaseFilter %{_bindir}/TargetedFileConverter %{_bindir}/FileFilter %{_bindir}/IDDecoyProbability %{_bindir}/OpenMSInfo %{_bindir}/ExternalCalibration %{_bindir}/OpenSwathFileSplitter %{_bindir}/MultiplexResolver %{_bindir}/TICCalculator %{_bindir}/PhosphoScoring %{_bindir}/INIUpdater %{_bindir}/RNPxlXICFilter %{_bindir}/FuzzyDiff %{_bindir}/XMLValidator %{_bindir}/SemanticValidator %{_bindir}/CVInspector %{_bindir}/IDSplitter %{_bindir}/OpenSwathMzMLFileCacher %{_bindir}/Digestor %{_bindir}/DigestorMotif %{_bindir}/DecoyDatabase %{_bindir}/SequenceCoverageCalculator %{_bindir}/IDExtractor %{_bindir}/IDMassAccuracy %{_bindir}/SpecLibCreator %{_bindir}/ERPairFinder %{_bindir}/MRMPairFinder %{_bindir}/ImageCreator %{_bindir}/MassCalculator %{_bindir}/DeMeanderize %{_bindir}/OpenSwathDIAPreScoring %{_bindir}/OpenSwathRewriteToFeatureXML %{_bindir}/AccurateMassSearch %{_bindir}/QCCalculator %{_bindir}/QCImporter %{_bindir}/QCEmbedder %{_bindir}/QCExporter %{_bindir}/QCExtractor %{_bindir}/QCMerger %{_bindir}/QCShrinker %{_bindir}/TriqlerConverter %{_bindir}/FLASHDeconv %{_bindir}/FLASHDeconvWizard %{_bindir}/JSONExporter %files data %doc CHANGELOG AUTHORS README* CODE_OF_CONDUCT.md %license LICENSE* %{_datadir}/OpenMS/ %files doc %doc CHANGELOG AUTHORS README* CODE_OF_CONDUCT.md %license LICENSE* %doc html %files devel %license LICENSE* %doc CHANGELOG AUTHORS README* CODE_OF_CONDUCT.md %if %{with check} %{_bindir}/*_test %endif %{_includedir}/OpenMS/ %if 0%{?with_pyOpenMS} %files -n python3-openms %license License.txt %doc src/pyOpenMS/README_WRAPPING_NEW_CLASSES %{python3_sitearch}/pyopenms/ %{python3_sitearch}/pyopenms-*.egg-info/ %endif %changelog * Sun Nov 05 2023 Antonio Trande - 1:3.1.0-0.4.pre1 - Exclude failed test in aarch64 * Sun Oct 29 2023 Antonio Trande - 1:3.1.0-0.3.pre1 - Add missing binary file * Sun Oct 29 2023 Antonio Trande - 1:3.1.0-0.2.pre1 - Fix installed files * Sat Oct 28 2023 Antonio Trande - 1:3.1.0-0.1.pre1 - Pre-release 3.1.0 * Mon Aug 14 2023 Antonio Trande - 3.0.0-15 - Fix unintentional change * Mon Aug 14 2023 Antonio Trande - 3.0.0-14 - Add runtime dependency (RHBZ#2231587) * Mon Aug 14 2023 Antonio Trande - 3.0.0-13 - Unbundle Qt5QuickWidgets libraries (RHBZ#2231587) * Sun Jul 30 2023 Antonio Trande - 3.0.0-12 - Exclude TOPP_OpenSwathWorkflow* tests * Sun Jul 30 2023 Antonio Trande - 3.0.0-11 - Exclude TOPP_OpenSwathWorkflow_14_out1 test * Sat Jul 29 2023 Antonio Trande - 3.0.0-10 - Remove Exit 1 * Mon Jul 24 2023 Antonio Trande - 3.0.0-9 - Disable LTO flags * Sun Jul 23 2023 Antonio Trande - 3.0.0-8 - Set _smp_ncpus_max equal to 2 for all architectures * Sat Jul 22 2023 Antonio Trande - 3.0.0-7 - Use one job to build pyopenms * Fri Jul 21 2023 Antonio Trande - 3.0.0-6 - Release 3.0.0 * Thu Jul 20 2023 Fedora Release Engineering - 3.0.0-5 - Rebuilt for https://fedoraproject.org/wiki/Fedora_39_Mass_Rebuild * Mon Jul 03 2023 Antonio Trande - 3.0.0-4 - Add new tool and CMake config files * Sun Jul 02 2023 Antonio Trande - 3.0.0-3 - Fix macro * Sun Jul 02 2023 Antonio Trande - Exclude failed tests * Sun Jul 02 2023 Antonio Trande - 3.0.0-1 - Pre-release 3.0.0 * Wed Feb 01 2023 Antonio Trande - 2.8.0-7 - Fixed for GCC-13 * Thu Jan 19 2023 Fedora Release Engineering - 2.8.0-6 - Rebuilt for https://fedoraproject.org/wiki/Fedora_38_Mass_Rebuild * Fri Aug 19 2022 Jerry James - 2.8.0-5 - Rebuild for libsvm 3.3 * Fri Jul 22 2022 Fedora Release Engineering - 2.8.0-4 - Rebuilt for https://fedoraproject.org/wiki/Fedora_37_Mass_Rebuild * Sat Mar 05 2022 Antonio Trande - 2.8.0-3 - Pre-release 2.8.0| ExclusiveArch qt5_qtwebengine_arches * Sat Mar 05 2022 Antonio Trande - 2.8.0-2 - Pre-release 2.8.0| Remove unused files * Sat Mar 05 2022 Antonio Trande - 2.8.0-1 - Pre-release 2.8.0| Patched for GCC-12 * Thu Jan 20 2022 Fedora Release Engineering - 2.7.0-18 - Rebuilt for https://fedoraproject.org/wiki/Fedora_36_Mass_Rebuild * Sun Nov 28 2021 Antonio Trande - 2.7.0-17 - Disable Python binding * Thu Nov 25 2021 Orion Poplawski - 2.7.0-16 - Use %%make_build to allow _smp_ncpus_max to work * Tue Nov 23 2021 Orion Poplawski - 2.7.0-15 - Limit to 2 cpus on %%{ix86} to limit memory usage * Sun Nov 21 2021 Orion Poplawski - 2.7.0-14 - Rebuild for hdf5 1.12.1 * Tue Sep 21 2021 Antonio Trande - 2.7.0-13 - Restore default flags in i686 arch * Tue Sep 21 2021 Antonio Trande - 2.7.0-12 - Disable LTO flags in i686 arch * Sun Sep 19 2021 Antonio Trande - 2.7.0-11 - Remove -Wp,-D_GLIBCXX_ASSERTIONS flag on i686 * Sun Sep 19 2021 Antonio Trande - 2.7.0-10 - Remove -pipe flag on i686 * Sun Sep 19 2021 Antonio Trande - 2.7.0-9 - Reduce optimization level further on i686 * Sun Sep 19 2021 Antonio Trande - 2.7.0-8 - Disable debug build | Reduce optimization level on i686 * Sun Sep 19 2021 Antonio Trande - 2.7.0-7 - Enable debug build * Sat Sep 18 2021 Antonio Trande - 2.7.0-6 - Release 2.7.0 | Use bundled seqan (optimized for OpenMS) * Sat Sep 18 2021 Antonio Trande - 2.7.0-5 - Release 2.7.0 | Unbundle seqan /2 * Sat Sep 18 2021 Antonio Trande - 2.7.0-4 - Release 2.7.0 | Unbundle seqan * Sat Sep 18 2021 Antonio Trande - 2.7.0-3 - Release 2.7.0 | Tests disabled * Sat Sep 18 2021 Antonio Trande - 2.7.0-2 - Obsolete old patches * Sat Sep 18 2021 Antonio Trande - 2.7.0-1 - Release 2.7.0 * Tue Aug 10 2021 Orion Poplawski - 2.6.0-39 - Rebuild for hdf5 1.10.7 * Sat Aug 07 2021 Jonathan Wakely - 2.6.0-38 - Rebuilt for Boost 1.76 * Thu Jul 22 2021 Fedora Release Engineering - 2.6.0-37 - Rebuilt for https://fedoraproject.org/wiki/Fedora_35_Mass_Rebuild * Tue Jun 22 2021 Antonio Trande - 2.6.0-36 - Patched for upstream bug #5381 * Sat Jun 19 2021 Antonio Trande - 2.6.0-35 - Disable Python binding in ARM and s390x * Sat Jun 19 2021 Antonio Trande - 2.6.0-34 - Set job 1 when compiling Python libraries * Sat Jun 19 2021 Antonio Trande - 2.6.0-33 - Downgrade Make jobs for building in all architectures * Sat Jun 19 2021 Antonio Trande - 2.6.0-32 - Use ctest * Sat Jun 19 2021 Antonio Trande - 2.6.0-31 - Fix rpath errors * Fri Jun 18 2021 Antonio Trande - 2.6.0-30 - Release mode| Fix directory of executable test files * Fri Jun 18 2021 Antonio Trande - 2.6.0-29 - Release mode| Enable Python binding| Enable check * Fri Jun 18 2021 Antonio Trande - 2.6.0-28 - Release mode| Disable LTO flags * Fri Jun 18 2021 Antonio Trande - 2.6.0-27 - Add ldflags in debug mode * Fri Jun 18 2021 Antonio Trande - 2.6.0-26 - Re-enable debuginfo package * Fri Jun 18 2021 Antonio Trande - 2.6.0-25 - Add -g flags * Fri Jun 18 2021 Antonio Trande - 2.6.0-24 - Disable debuginfo package in debug mode * Fri Jun 18 2021 Antonio Trande - 2.6.0-23 - Switch to debug build /4 * Fri Jun 18 2021 Antonio Trande - 2.6.0-22 - Switch to debug build /3 * Fri Jun 18 2021 Antonio Trande - 2.6.0-21 - Switch to debug build /2 * Fri Jun 18 2021 Antonio Trande - 2.6.0-20 - Switch to debug build| Fix installation of test files * Fri Jun 18 2021 Antonio Trande - 2.6.0-19 - Switch to debug build * Thu Jun 17 2021 Antonio Trande - 2.6.0-18 - Increase Make jobs * Thu Jun 17 2021 Antonio Trande - 2.6.0-17 - Modify CMake options for testing * Thu Jun 17 2021 Antonio Trande - 2.6.0-16 - Change directory of the Python installation scripts| Enable tests * Wed Jun 16 2021 Antonio Trande - 2.6.0-15 - Importing built-in env python module /2 * Wed Jun 16 2021 Antonio Trande - 2.6.0-14 - Importing built-in env python mmodule * Wed Jun 16 2021 Antonio Trande - 2.6.0-13 - Enable Python binding * Wed Feb 17 2021 Antonio T - 2.6.0-12 - Filter private libraries * Tue Feb 16 2021 Antonio T - 2.6.0-11 - Remove popd * Tue Feb 16 2021 Antonio T - 2.6.0-10 - Remove fido-pi dependencies * Tue Feb 02 2021 Antonio T - 2.6.0-9 - Patch GLPK version * Tue Jan 26 2021 Fedora Release Engineering - 2.6.0-8 - Rebuilt for https://fedoraproject.org/wiki/Fedora_34_Mass_Rebuild * Fri Jan 22 2021 Jonathan Wakely - 2.6.0-7 - Rebuilt for Boost 1.75 * Thu Jan 07 2021 Tom Stellard - 2.6.0-6 - Add BuildRequires: make * Sun Oct 25 2020 sagitter - 2.6.0-5 - Fix rpaths * Sun Oct 25 2020 sagitter - 2.6.0-4 - Avoid skipping rpaths * Fri Oct 02 2020 sagitter - 2.6.0-3 - Add new binary files * Fri Oct 02 2020 sagitter - 2.6.0-2 - Remove old binary files * Fri Oct 02 2020 sagitter - 2.6.0-1 - Release 2.6.0 * Sat Aug 01 2020 sagitter - 2.5.0-11 - Enable cmake_in_source_build * Sat Aug 01 2020 Fedora Release Engineering - 2.5.0-10 - Second attempt - Rebuilt for https://fedoraproject.org/wiki/Fedora_33_Mass_Rebuild * Tue Jul 28 2020 Fedora Release Engineering - 2.5.0-9 - Rebuilt for https://fedoraproject.org/wiki/Fedora_33_Mass_Rebuild * Thu Jun 25 2020 Orion Poplawski - 2.5.0-8 - Rebuild for hdf5 1.10.6 * Wed Jun 03 2020 sagitter - 2.5.0-7 - Patched for upstream bug #4765 * Tue Jun 02 2020 sagitter - 2.5.0-6 - Rebuild for boost-1.73 * Fri May 01 2020 sagitter - 2.5.0-5 - Rebuild for coin-or-* updates * Tue Feb 25 2020 sagitter - 2.5.0-4 - Fix desktop-file-install command * Tue Feb 25 2020 sagitter - 2.5.0-3 - Add Desktop file's categories * Tue Feb 25 2020 sagitter - 2.5.0-2 - Fix Changelog * Tue Feb 25 2020 sagitter - 2.5.0-1 - Release 2.5.0 * Wed Jan 29 2020 Fedora Release Engineering - 2.4.0-8 - Rebuilt for https://fedoraproject.org/wiki/Fedora_32_Mass_Rebuild * Sun Sep 08 2019 sagitter - 2.4.0-7 - Rebuild for autowrap-0.19.1 * Thu Jul 25 2019 Fedora Release Engineering - 2.4.0-6 - Rebuilt for https://fedoraproject.org/wiki/Fedora_31_Mass_Rebuild * Fri Jun 28 2019 Jerry James - 2.4.0-5 - Rebuild for coin-or package updates. * Fri Feb 01 2019 Fedora Release Engineering - 2.4.0-4 - Rebuilt for https://fedoraproject.org/wiki/Fedora_30_Mass_Rebuild * Wed Jan 30 2019 Jonathan Wakely - 2.4.0-3 - Rebuilt for Boost 1.69 * Tue Nov 06 2018 sagitter - 2.4.0-2 - Add rpmlintrc file * Fri Nov 02 2018 sagitter - 2.4.0-1 - Release 2.4.0 * Wed Aug 22 2018 sagitter - 2.3.0-22 - Patched for removing unrecognized command line options * Wed Aug 22 2018 sagitter - 2.3.0-21 - Deprecate Python2 binding of fedora 30+ * Fri Jul 13 2018 Fedora Release Engineering - 2.3.0-20 - Rebuilt for https://fedoraproject.org/wiki/Fedora_29_Mass_Rebuild * Tue Jun 19 2018 Miro Hrončok - 2.3.0-19 - Rebuilt for Python 3.7 * Sat Jun 02 2018 Jerry James - 2.3.0-18 - Rebuild for glpk 4.65. * Thu Mar 08 2018 Adam Williamson - 2.3.0-17 - Rebuild to fix GCC 8 mis-compilation * Mon Feb 12 2018 sagitter - 2.3.0-16 - Fix XML file's permissions * Mon Feb 12 2018 sagitter - 2.3.0-15 - Replace make_install macros * Mon Feb 12 2018 sagitter - 2.3.0-14 - Fix standard permissions * Sun Feb 11 2018 sagitter - 2.3.0-13 - Fix script paths * Sun Feb 11 2018 sagitter - 2.3.0-12 - Fix typo * Sun Feb 11 2018 sagitter - 2.3.0-11 - Fix wrong-script-end-of-line-encoding warnings * Sun Feb 11 2018 sagitter - 2.3.0-10 - Fix R scripts shebang * Sun Feb 11 2018 sagitter - 2.3.0-9 - Compile pyOpenMS * Thu Feb 08 2018 Fedora Release Engineering - 2.3.0-8 - Rebuilt for https://fedoraproject.org/wiki/Fedora_28_Mass_Rebuild * Mon Feb 05 2018 sagitter - 2.3.0-7 - Rebuild for boost-1.66 * Wed Jan 10 2018 sagitter - 2.3.0-6 - Set maximum required version of seqan * Fri Jan 05 2018 sagitter - 2.3.0-5 - Fix typos * Fri Jan 05 2018 sagitter - 2.3.0-4 - Tests disabled * Fri Jan 05 2018 sagitter - 2.3.0-3 - Fix R script * Thu Jan 04 2018 sagitter - 2.3.0-2 - Fix list of tools * Thu Jan 04 2018 sagitter - 2.3.0-1 - Update to OpenMS-2.3.0 * Thu Dec 21 2017 sagitter - 2.2.0-9 - Appdata file moved into metainfo data directory * Sat Nov 18 2017 sagitter - 2.2.0-8 - Rebuild OpenMS-2.2.0 * Fri Oct 13 2017 sagitter - 2.2.0-7 - Rebuild for wildmagic5-5.17 * Thu Jul 27 2017 Fedora Release Engineering - 2.2.0-6 - Rebuilt for https://fedoraproject.org/wiki/Fedora_27_Mass_Rebuild * Mon Jul 24 2017 Björn Esser - 2.2.0-5 - Rebuilt for Boost 1.64 * Sun Jul 23 2017 sagitter - 2.2.0-4 - Fix strip num of patch4 * Sun Jul 23 2017 sagitter - 2.2.0-3 - Fix compatiblity with boost-1.64 * Sun Jul 23 2017 sagitter - 2.2.0-2 - Rebuild for boost-1.64 * Fri Jul 07 2017 sagitter - 2.2.0-1 - Update to 2.2.0 * Sun Jun 11 2017 sagitter - 2.1.0-18 - Rebuild for wildmagic5-5.15 * Fri Apr 14 2017 sagitter - 2.1.0-17 - Rebuild for biopython-1.69 * Wed Apr 05 2017 Jerry James - 2.1.0-16 - Rebuild for glpk 4.61 * Tue Feb 07 2017 sagitter - 2.1.0-15 - Rebuild for boost-1.63 * Wed Feb 01 2017 sagitter - 2.1.0-14 - Rebuild for GCC-7.0.1 * Fri Jan 27 2017 Jonathan Wakely - 2.1.0-13 - Rebuilt for Boost 1.63 * Fri Jan 06 2017 sagitter - 2.1.0-12 - Fix desktop icons * Wed Dec 28 2016 Rich Mattes - 2.1.0-11 - Rebuild for eigen3-3.3.1 * Tue Nov 22 2016 sagitter - 2.1.0-10 - Drop old patch * Tue Nov 22 2016 sagitter - 2.1.0-9 - Update to 2.1.0 (stable release) * Thu Nov 10 2016 sagitter - 2.1.0-8 - Add LuciphorAdapter command * Thu Nov 10 2016 sagitter - 2.1.0-7 - Make jobs increased * Thu Nov 10 2016 sagitter - 2.1.0-6 - Python bindings disabled (upstream issue #2286) * Thu Nov 10 2016 sagitter - 2.1.0-5 - Build jobs limited to 1 globally * Thu Nov 10 2016 sagitter - 2.1.0-4 - Build jobs limited to 1 for Python * Thu Nov 10 2016 sagitter - 2.1.0-3 - Build jobs limited to 2 for Python * Thu Nov 10 2016 sagitter - 2.1.0-2 - Patched to fix PyOpenMS * Tue Nov 08 2016 sagitter - 2.1.0-1 - Update to 2.1.0 * Tue Jul 19 2016 Fedora Release Engineering - 2.0.0-41 - https://fedoraproject.org/wiki/Changes/Automatic_Provides_for_Python_RPM_ Packages * Fri Jun 24 2016 sagitter - 2.0.0-40 - Rebuild for Biopython-1.67 * Tue May 17 2016 Jonathan Wakely - 2.0.0-39 - Rebuilt for linker errors in boost (#1331983) * Sat Mar 12 2016 sagitter - 2.0.0-38 - Rebuild for GLPK-4.59 * Fri Feb 19 2016 sagitter - 2.0.0-37 - Rebuild for GLPK-4.58 * Mon Feb 15 2016 sagitter - 2.0.0-36 - Macros removed from Obsolets tags * Sun Feb 14 2016 sagitter - 2.0.0-35 - PyOpenMS disabled on x86 arches * Sun Feb 14 2016 sagitter - 2.0.0-34 - Patched for GCC-6 * Thu Feb 04 2016 Fedora Release Engineering - 2.0.0-33 - Rebuilt for https://fedoraproject.org/wiki/Fedora_24_Mass_Rebuild * Wed Jan 27 2016 sagitter - 2.0.0-32 - Fixed package dependency * Tue Jan 26 2016 sagitter - 2.0.0-31 - Data sub-package arched * Mon Jan 25 2016 sagitter - 2.0.0-30 - Disabled HAS_XSERVER option * Sun Jan 24 2016 sagitter - 2.0.0-29 - Update to commit #6f51b3 * Mon Dec 14 2015 sagitter - 2.0.0-28 - Update to commit #f19f8b; Python3 binding * Thu Nov 05 2015 sagitter - 2.0.0-27 - Hardened builds on - 2.0.0-26 - Rebuilt for Boost 1.59 * Wed Jul 29 2015 Dennis Gilmore - 2.0.0-25 - Rebuilt for https://fedoraproject.org/wiki/Changes/F23Boost159 * Fri Jul 24 2015 sagitter - 2.0.0-24 - Rebuild again * Tue Jul 21 2015 sagitter - 2.0.0-23 - Rebuild for Boost upgrade to 1.58.0 * Thu Jun 18 2015 Dennis Gilmore - 2.0.0-22 - Rebuilt for https://fedoraproject.org/wiki/Fedora_23_Mass_Rebuild * Fri Jun 12 2015 sagitter - 2.0.0-21 - memleak test excluded again * Tue Jun 09 2015 sagitter - 2.0.0-20 - Exclude TOPP_OpenSwathAssayGenerator_test_1_out1 test * Tue Jun 09 2015 sagitter - 2.0.0-19 - Exclude TOPP_OpenSwathAssayGenerator_test_1_out1 test * Tue Jun 09 2015 sagitter - 2.0.0-18 - Update to the post-release #88dc25 * Fri May 15 2015 sagitter - 2.0.0-17 - Bug fix in upstream desktop files * Fri May 15 2015 sagitter - 2.0.0-16 - Set environment variables in desktop files * Fri May 08 2015 sagitter - 2.0.0-15 - Excluded TOPP_XTandemAdapter_ test * Fri May 08 2015 sagitter - 2.0.0-14 - Excluded TOPP_XTandemAdapter_ test * Fri May 08 2015 sagitter - 2.0.0-13 - Rebuild after XTandem update. * Sat May 02 2015 sagitter - 2.0.0-12 - memleaks test excluded * Sat May 02 2015 sagitter - 2.0.0-11 - memleaks test excluded * Sat May 02 2015 sagitter - 2.0.0-10 - PyOpenMS compiled without parallel make; PyOpenMS tests disabled. * Sat May 02 2015 sagitter - 2.0.0-9 - PyOpenMS compiled without parallel make; PyOpenMS tests disabled. * Fri May 01 2015 sagitter - 2.0.0-8 - Source archive re-compressed by upstream * Fri May 01 2015 sagitter - 2.0.0-7 - Source archive re-compressed by upstream * Fri May 01 2015 sagitter - 2.0.0-6 - SPEC cleanups * Thu Apr 30 2015 sagitter - 2.0.0-5 - Patched pyOpenMS version definition * Thu Apr 30 2015 sagitter - 2.0.0-4 - Patched pyOpenMS version definition * Thu Apr 30 2015 sagitter - 2.0.0-3 - PyOpenMS is still compiled against Python2 on Linux * Thu Apr 30 2015 sagitter - 2.0.0-2 - PyOpenMS is still compiled against Python2 on Linux * Thu Apr 30 2015 sagitter - 2.0.0-1 - Update to the release 2.0 * Mon Jan 26 2015 Petr Machata - 1.11.1-4 - Rebuild for boost 1.57.0 * Sat Dec 13 2014 sagitter - 1.11.1-3 - Parallel make disabled. * Fri Dec 12 2014 sagitter - 1.11.1-2 - Parallel make disabled on Fedora 20. * Fri Dec 12 2014 sagitter - 1.11.1-1 - New package.