#%%global checkout bde813c6c20588a953d3295f759b834398747e8b #%%global date 20170131 %global with_py2OpenMS 0 %global with_py3OpenMS 0 # Python bindings disabled for memory issue # https://github.com/OpenMS/OpenMS/issues/2286 Obsoletes: python2-openms <= 0:2.1.0-0.1 Obsoletes: python3-openms <= 0:2.1.0-0.1 Name: openms Summary: LC/MS data management and analyses Version: 2.2.0 Release: 4%{?dist} License: BSD URL: http://www.openms.de/ Source0: https://github.com/OpenMS/OpenMS/archive/Release%{version}.tar.gz#/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: qt-devel BuildRequires: qt-x11 BuildRequires: qtwebkit-devel BuildRequires: cmake 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: libsvm-devel BuildRequires: gsl-devel BuildRequires: glpk-devel BuildRequires: xerces-c-devel BuildRequires: boost-devel BuildRequires: seqan-devel BuildRequires: sqlite-devel BuildRequires: wildmagic5-devel BuildRequires: zlib-devel BuildRequires: bzip2-devel BuildRequires: tbb-devel BuildRequires: eigen3-devel BuildRequires: desktop-file-utils BuildRequires: fido-pi BuildRequires: libappstream-glib ## Build documentation ## Doxygen useful only on SVN versions BuildRequires: doxygen, dos2unix, graphviz BuildRequires: texlive, ImageMagick, texlive-a4wide, texlive-xtab ##Xvfb is needed to run a virtual X server used by some tests BuildRequires: xorg-x11-server-Xvfb, gnuplot Requires: fido-pi Requires: %{name}-data%{?_isa} = %{version}-%{release} ##Remove -O0 flag for tests compiling Patch0: %{name}-remove_testflag.patch ##Fix SyntaxError: in Python3 Patch1: %{name}-fix_print_error.patch ##Fix GCC 7 error # https://github.com/OpenMS/OpenMS/issues/2750 Patch2: %{name}-%{version}-gcc7-2756.patch Patch3: %{name}-%{version}-fix-warnings-2757.patch # https://github.com/OpenMS/OpenMS/issues/2790 Patch4: %{name}-%{version}-fix-boost.164.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 tools Summary: OpenMS tools Requires: %{name}-data%{?_isa} = %{version}-%{release} %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 %if 0%{?with_py2OpenMS} %package -n python2-openms Summary: OpenMS Python2 bindings %{?python_provide:%python_provide python2-%{name}} BuildRequires: python-setuptools BuildRequires: python2-devel BuildRequires: numpy BuildRequires: python-nose BuildRequires: python2-autowrap >= 0.8.0 BuildRequires: Cython, python-wheel BuildRequires: python-biopython Requires: python-biopython Requires: %{name}-data%{?_isa} = %{version}-%{release} Requires: %{name}%{?_isa} = %{version}-%{release} %description -n python2-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). %endif %if 0%{?with_py3OpenMS} %package -n python3-openms Summary: OpenMS Python3 bindings %{?python_provide:%python_provide python3-%{name}} BuildRequires: python3-setuptools BuildRequires: python3-devel BuildRequires: python3-numpy BuildRequires: python3-nose BuildRequires: python3-autowrap >= 0.8.0 BuildRequires: python3-Cython BuildRequires: python3-wheel BuildRequires: python3-biopython Requires: %{name}-data%{?_isa} = %{version}-%{release} Requires: %{name}%{?_isa} = %{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 %description devel OpenMS development files. %package data Summary: The OpenMS data files %description data The OpenMS data files. %package doc Summary: OpenMS documentation BuildArch: noarch %description doc HTML documentation of OpenMS. %prep %setup -qc mv OpenMS-Release%{version} py2build pushd py2build rm -rf cmake/MacOSX ## Strip all .png files ## 'iCCP: known incorrect sRGB profile' warnings find . -type f -name "*.png" -exec convert {} -strip {} \; %patch0 -p0 %if 0%{?fedora} > 25 %patch2 -p1 %endif %patch3 -p1 %if 0%{?fedora} > 26 %patch4 -p0 %endif # Remove invalid tags sed -e 's| ||g' -i share/OpenMS/DESKTOP/*.appdata.xml popd %if 0%{?with_py3OpenMS} cp -a py2build py3build pushd py3build dos2unix share/OpenMS/examples/simulation/FASTAProteinAbundanceSampling.py %patch1 -p0 popd %endif %build pushd py2build mkdir -p build && cd build export LDFLAGS="%{__global_ldflags} -Wl,-z,now -Wl,--as-needed" %cmake -Wno-dev -DCMAKE_CXX_COMPILER_VERSION:STRING=$(gcc -dumpversion) \ -DCMAKE_COLOR_MAKEFILE:BOOL=ON -DBUILD_TESTING:BOOL=ON -DBUILD_EXAMPLES:BOOL=ON -DENABLE_TOPP_TESTING:BOOL=ON -DENABLE_CLASS_TESTING:BOOL=ON \ -DCMAKE_CXX_FLAGS_RELEASE:STRING="-Wno-cpp $RPM_OPT_FLAGS -Wl,-z,relro -Wl,-z,now" -DCMAKE_C_FLAGS_RELEASE:STRING="-Wno-cpp $RPM_OPT_FLAGS -Wl,-z,relro -Wl,-z,now " \ -DCMAKE_VERBOSE_MAKEFILE=TRUE -DCMAKE_PREFIX_PATH=%{_prefix} \ -DENABLE_SVN=OFF -DCMAKE_BUILD_TYPE=Release -DBOOST_USE_STATIC=OFF \ -DCMAKE_SKIP_RPATH:BOOL=TRUE -DCMAKE_SKIP_INSTALL_RPATH:BOOL=YES \ -DMT_ENABLE_OPENMP=ON -DENABLE_GCC_WERROR:BOOL=OFF \ -DFIDO_BINARY:FILEPATH=%{_bindir}/Fido -DFIDOCHOOSEPARAMS_BINARY:FILEPATH=%{_bindir}/FidoChooseParameters \ -DBOOST_USE_STATIC:BOOL=OFF -DBoost_INCLUDE_DIR:PATH=%{_includedir} \ -DBoost_IOSTREAMS_LIBRARY_RELEASE:FILEPATH=%{_libdir}/libboost_iostreams.so \ -DBoost_MATH_C99_LIBRARY_RELEASE:FILEPATH=%{_libdir}/libboost_math_c99.so \ -DBoost_REGEX_LIBRARY_RELEASE:FILEPATH=%{_libdir}/libboost_regex.so \ -DENABLE_TUTORIALS:BOOL=OFF -DENABLE_UNITYBUILD:BOOL=OFF \ -DHAS_XSERVER:BOOL=OFF \ -DCMAKE_INSTALL_PREFIX=%{_prefix} \ -DINSTALL_BIN_DIR:PATH=bin -DINSTALL_CMAKE_DIR:PATH=%{_lib}/cmake/OpenMS \ -DINSTALL_DOC_DIR:PATH=share/doc/openms-doc -DINSTALL_INCLUDE_DIR:PATH=include \ -DINSTALL_LIB_DIR:PATH=%{_lib}/OpenMS -DINSTALL_SHARE_DIR:PATH=share/OpenMS \ -DPACKAGE_TYPE:STRING=none -DWITH_GUI:BOOL=ON \ -DXercesC_INCLUDE_DIRS:PATH=%{_includedir}/xercesc \ -DXercesC_LIBRARY_RELEASE:FILEPATH=%{_libdir}/libxerces-c.so \ -DOPENMS_DISABLE_UPDATE_CHECK:BOOL=OFF -DENABLE_UPDATE_CHECK:BOOL=OFF -DGIT_TRACKING:BOOL=OFF \ %if %{?__isa_bits:%{__isa_bits}}%{!?__isa_bits:32} == 64 -DOPENMS_64BIT_ARCHITECTURE:BOOL=ON \ %else -DOPENMS_64BIT_ARCHITECTURE:BOOL=OFF \ %endif %if 0%{?with_py2OpenMS} -DPYOPENMS=ON -DPYTHON_EXECUTABLE:FILEPATH=%{__python2} \ -DCYTHON_EXECUTABLE:FILEPATH=%{_bindir}/cython .. %else -DPYOPENMS=OFF .. %endif make --jobs 4 OpenMS TOPP UTILS GUI %if 0%{?with_py2OpenMS} make --jobs 1 pyopenms %endif cd .. popd ##Python3 bindings %if 0%{?with_py3OpenMS} pushd py3build mkdir -p build && cd build export LDFLAGS="%{__global_ldflags} -Wl,-z,now -Wl,--as-needed" %cmake -Wno-dev -DCMAKE_CXX_COMPILER_VERSION:STRING=$(gcc -dumpversion) \ -DCMAKE_COLOR_MAKEFILE:BOOL=ON -DBUILD_TESTING:BOOL=OFF -DBUILD_EXAMPLES:BOOL=OFF -DENABLE_TOPP_TESTING:BOOL=OFF -DENABLE_CLASS_TESTING:BOOL=OFF \ -DCMAKE_CXX_FLAGS_RELEASE:STRING="-Wno-cpp $RPM_OPT_FLAGS -Wl,-z,relro -Wl,-z,now" -DCMAKE_C_FLAGS_RELEASE:STRING="-Wno-cpp $RPM_OPT_FLAGS -Wl,-z,relro -Wl,-z,now " \ -DCMAKE_VERBOSE_MAKEFILE=TRUE -DCMAKE_PREFIX_PATH=%{_prefix} \ -DENABLE_SVN=OFF -DCMAKE_BUILD_TYPE=Release -DBOOST_USE_STATIC=OFF \ -DCMAKE_SKIP_RPATH:BOOL=TRUE -DCMAKE_SKIP_INSTALL_RPATH:BOOL=YES \ -DMT_ENABLE_OPENMP=ON -DENABLE_GCC_WERROR:BOOL=OFF \ -DFIDO_BINARY:FILEPATH=%{_bindir}/Fido -DFIDOCHOOSEPARAMS_BINARY:FILEPATH=%{_bindir}/FidoChooseParameters \ -DBOOST_USE_STATIC:BOOL=OFF -DBoost_INCLUDE_DIR:PATH=%{_includedir} \ -DBoost_IOSTREAMS_LIBRARY_RELEASE:FILEPATH=%{_libdir}/libboost_iostreams.so \ -DBoost_MATH_C99_LIBRARY_RELEASE:FILEPATH=%{_libdir}/libboost_math_c99.so \ -DBoost_REGEX_LIBRARY_RELEASE:FILEPATH=%{_libdir}/libboost_regex.so \ -DENABLE_TUTORIALS:BOOL=OFF -DENABLE_UNITYBUILD:BOOL=OFF \ -DHAS_XSERVER:BOOL=OFF \ -DCMAKE_INSTALL_PREFIX=%{_prefix} \ -DINSTALL_BIN_DIR:PATH=bin -DINSTALL_CMAKE_DIR:PATH=%{_lib}/cmake/OpenMS \ -DINSTALL_DOC_DIR:PATH=share/doc/openms-doc -DINSTALL_INCLUDE_DIR:PATH=include \ -DINSTALL_LIB_DIR:PATH=%{_lib}/OpenMS -DINSTALL_SHARE_DIR:PATH=share/OpenMS \ -DPACKAGE_TYPE:STRING=none -DWITH_GUI:BOOL=ON \ -DXercesC_INCLUDE_DIRS:PATH=%{_includedir}/xercesc \ -DXercesC_LIBRARY_RELEASE:FILEPATH=%{_libdir}/libxerces-c.so \ -DOPENMS_DISABLE_UPDATE_CHECK:BOOL=OFF -DENABLE_UPDATE_CHECK:BOOL=OFF -DGIT_TRACKING:BOOL=OFF \ %if %{?__isa_bits:%{__isa_bits}}%{!?__isa_bits:32} == 64 -DOPENMS_64BIT_ARCHITECTURE:BOOL=ON \ %else -DOPENMS_64BIT_ARCHITECTURE:BOOL=OFF \ %endif -DPYOPENMS=ON -DPYTHON_EXECUTABLE:FILEPATH=%{__python3} \ -DCYTHON_EXECUTABLE:FILEPATH=%{_bindir}/cython3 .. make --jobs 4 OpenMS TOPP UTILS GUI make --jobs 1 pyopenms cd .. popd %endif ##if with_py3OpenMS %install pushd py2build/build export LD_LIBRARY_PATH=$PWD/lib:$LD_LIBRARY_PATH xvfb-run -a make install DESTDIR=%{buildroot} %if 0%{?with_py2OpenMS} ## pyOpenMS installation cd pyOpenMS %{__python2} setup.py install --skip-build --root %{buildroot} ln -s -f %{_libdir}/OpenMS/libOpenMS.so %{buildroot}%{python2_sitearch}/pyopenms/libOpenMS.so ln -s -f %{_libdir}/OpenMS/libOpenSwathAlgo.so %{buildroot}%{python2_sitearch}/pyopenms/libOpenSwathAlgo.so ln -s -f %{_libdir}/OpenMS/libSuperHirn.so %{buildroot}%{python2_sitearch}/pyopenms/libSuperHirn.so ## Fix standard permissions chmod 0755 %{buildroot}%{python2_sitearch}/pyopenms/pyopenms.so cd .. %endif popd %if 0%{?with_py3OpenMS} pushd py3build/build export LD_LIBRARY_PATH=$PWD/lib:$LD_LIBRARY_PATH xvfb-run -a make install DESTDIR=%{buildroot} cd pyOpenMS %{__python3} setup.py install --skip-build --root %{buildroot} 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 cd .. popd %endif ##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 LD_LIBRARY_PATH=%{_libdir}/OpenMS OPENMS_DATA_PATH=%{_datadir}/OpenMS TOPPAS %U" \ --set-icon=%{_datadir}/icons/TOPP/TOPPAS.png \ --set-key=StartupNotify --set-value=true \ --dir=%{buildroot}%{_datadir}/applications py2build/share/OpenMS/DESKTOP/TOPPAS.desktop desktop-file-install \ --set-key=Exec --set-value="env LD_LIBRARY_PATH=%{_libdir}/OpenMS OPENMS_DATA_PATH=%{_datadir}/OpenMS TOPPView %U" \ --set-icon=%{_datadir}/icons/TOPP/TOPPView.png \ --set-key=StartupNotify --set-value=true \ --dir=%{buildroot}%{_datadir}/applications py2build/share/OpenMS/DESKTOP/TOPPView.desktop desktop-file-install \ --set-key=Exec --set-value="env LD_LIBRARY_PATH=%{_libdir}/OpenMS OPENMS_DATA_PATH=%{_datadir}/OpenMS INIFileEditor %U" \ --dir=%{buildroot}%{_datadir}/applications %{SOURCE4} ##Install appdata files mkdir -p %{buildroot}%{_datadir}/appdata install -pm 644 py2build/share/OpenMS/DESKTOP/*.appdata.xml %{buildroot}%{_datadir}/appdata ##HTML files copied ##I want package them by using %%doc macro cp -a %{buildroot}%{_datadir}/doc/openms-doc/html html cp -p %{buildroot}%{_datadir}/doc/openms-doc/index.html ./ rm -rf %{buildroot}%{_datadir}/doc/openms-doc/html rm -f %{buildroot}%{_datadir}/doc/openms-doc/index.html %post /bin/touch --no-create %{_datadir}/icons/TOPP &>/dev/null || : %postun if [ $1 -eq 0 ] ; then /bin/touch --no-create %{_datadir}/icons/TOPP &>/dev/null /usr/bin/gtk-update-icon-cache %{_datadir}/icons/TOPP &>/dev/null || : fi %posttrans /usr/bin/gtk-update-icon-cache %{_datadir}/icons/TOPP &>/dev/null || : %check appstream-util validate-relax --nonet %{buildroot}%{_datadir}/appdata/*.appdata.xml pushd py2build/build ## Make all test export LD_LIBRARY_PATH=$PWD/lib:$LD_LIBRARY_PATH export PATH=$PWD/bin:$PATH export OPENMS_DATA_PATH=$PWD/share/OpenMS:$OPENMS_DATA_PATH ## Run a Virtual X server waiting 3 seconds before ## starting tests xvfb-run -a ctest -V -R OpenMS_ --force-new-ctest-process %{?_smp_mflags} %files %{_bindir}/TOPPView %{_bindir}/TOPPAS %{_bindir}/INIFileEditor %{_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}/Resampler %{_bindir}/SpectraFilterBernNorm %{_bindir}/SpectraFilterMarkerMower %{_bindir}/SpectraFilterNLargest %{_bindir}/SpectraFilterNormalizer %{_bindir}/SpectraFilterParentPeakMower %{_bindir}/SpectraFilterScaler %{_bindir}/SpectraFilterSqrtMower %{_bindir}/SpectraFilterThresholdMower %{_bindir}/SpectraFilterWindowMower %{_bindir}/TOFCalibration %{_bindir}/AdditiveSeries %{_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}/CompNovo %{_bindir}/CompNovoCID %{_bindir}/InspectAdapter %{_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}/PeptideIndexer %{_bindir}/ProteinInference %{_bindir}/InclusionExclusionListCreator %{_bindir}/PrecursorIonSelector %{_bindir}/MRMMapper %{_bindir}/MetaProSIP %{_bindir}/OpenSwathDecoyGenerator %{_bindir}/OpenSwathChromatogramExtractor %{_bindir}/OpenSwathAnalyzer %{_bindir}/OpenSwathRTNormalizer %{_bindir}/OpenSwathFeatureXMLToTSV %{_bindir}/OpenSwathConfidenceScoring %{_bindir}/OpenSwathAssayGenerator %{_bindir}/PTModel %{_bindir}/PTPredict %{_bindir}/RTModel %{_bindir}/RTPredict %{_bindir}/GenericWrapper %{_bindir}/ExecutePipeline %{_bindir}/FeatureFinderIdentification %{_bindir}/FeatureFinderMultiplex %{_bindir}/FidoAdapter %{_bindir}/LowMemPeakPickerHiRes %{_bindir}/LowMemPeakPickerHiRes_RandomAccess %{_bindir}/MRMTransitionGroupPicker %{_bindir}/MSGFPlusAdapter %{_bindir}/MetaboliteSpectralMatcher %{_bindir}/OpenSwathWorkflow %{_bindir}/PeakPickerIterative %{_bindir}/SimpleSearchEngine %{_bindir}/TopPerc %{_bindir}/IDScoreSwitcher %{_bindir}/MzMLSplitter %{_bindir}/LuciphorAdapter %{_bindir}/DatabaseFilter %{_bindir}/FeatureLinkerUnlabeledKD %{_bindir}/RNPxlSearch %{_datadir}/appdata/*.appdata.xml %{_datadir}/applications/TOPPAS.desktop %{_datadir}/applications/TOPPView.desktop %{_datadir}/applications/inifileeditor.desktop %{_datadir}/icons/TOPP/ %{_libdir}/OpenMS/ %files tools %{_bindir}/RNPxlSearch %{_bindir}/SpectraSTSearchAdapter %{_bindir}/DatabaseFilter %{_bindir}/TargetedFileConverter %{_bindir}/FileFilter %{_bindir}/IDDecoyProbability %{_bindir}/IDEvaluatorGUI %{_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}/FFEval %{_bindir}/IDEvaluator %{_bindir}/LabeledEval %{_bindir}/RTEvaluation %{_bindir}/TransformationEvaluation %{_bindir}/Digestor %{_bindir}/DigestorMotif %{_bindir}/DecoyDatabase %{_bindir}/SequenceCoverageCalculator %{_bindir}/IDExtractor %{_bindir}/IDMassAccuracy %{_bindir}/SpecLibCreator %{_bindir}/RNPxl %{_bindir}/ERPairFinder %{_bindir}/MRMPairFinder %{_bindir}/FeatureFinderSuperHirn %{_bindir}/ImageCreator %{_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 %doc py2build/CHANGELOG py2build/AUTHORS py2build/README %license py2build/LICENSE %{_datadir}/OpenMS/ %files doc %doc py2build/CHANGELOG py2build/AUTHORS py2build/README %license py2build/LICENSE %doc html index.html %files devel %license py2build/LICENSE %doc py2build/CHANGELOG py2build/AUTHORS py2build/README %{_includedir}/OpenMS/ %if 0%{?with_py2OpenMS} %files -n python2-openms %license py2build/src/pyOpenMS/License.txt %{python2_sitearch}/pyopenms/ %{python2_sitearch}/pyopenms-*.egg-info/ %endif %if 0%{?with_py3OpenMS} %files -n python3-openms %license py3build/src/pyOpenMS/License.txt %{python3_sitearch}/pyopenms/ %{python3_sitearch}/pyopenms-*.egg-info/ %endif %changelog * Thu Jul 27 2017 Fedora Release Engineering - 2.2.0-4 - Rebuilt for https://fedoraproject.org/wiki/Fedora_27_Mass_Rebuild * Mon Jul 24 2017 Björn Esser - 2.2.0-3 - Rebuilt for Boost 1.64 * Sun Jul 23 2017 Antonio Trande - 2.2.0-2 - Rebuild for boost-1.64 * Wed Jun 28 2017 Antonio Trande - 2.2.0-1 - Update to 2.2.0 - Include patch for GCC-7 * Sat Jun 10 2017 Antonio Trande - 2.1.0-9.20170131gitbde813 - Rebuild for wildmagic5-5.15 * Fri Apr 14 2017 Antonio Trande - 2.1.0-8.20170131gitbde813 - Rebuild for biopython-1.69 * Wed Apr 05 2017 Jerry James - 2.1.0-7.20170131gitbde813 - Rebuild for glpk 4.61 * Tue Feb 07 2017 Antonio Trande - 2.1.0-6.20170131gitbde813 - Rebuild for boost-1.63 * Tue Jan 31 2017 Antonio Trande - 2.1.0-5.20170131gitbde813 - Rebuild for GCC-7.0.1 - Add CMAKE_CXX_COMPILER_VERSION option * Fri Jan 27 2017 Jonathan Wakely - 2.1.0-4 - Rebuilt for Boost 1.63 * Fri Jan 06 2017 Antonio Trande - 2.1.0-3 - Fix desktop icons * Wed Dec 28 2016 Rich Mattes - 2.1.0-2 - Rebuild for eigen3-3.3.1 * Tue Nov 22 2016 Antonio Trande - 2.1.0-1 - Update to 2.1.0 (stable release) - Drop old patch * Thu Nov 10 2016 Antonio Trande - 2.1.0-0.1 - Update to 2.1.0 (pre-release) - Patched to fix PyOpenMS - Python bindings disabled (upstream issue #2286) * Tue Jul 19 2016 Fedora Release Engineering - 2.0.0-35.20160121git6f51b3 - https://fedoraproject.org/wiki/Changes/Automatic_Provides_for_Python_RPM_Packages * Fri Jun 24 2016 Antonio Trande - 2.0.0-34.20160121git6f51b3 - Rebuild for Biopython-1.67 * Tue May 17 2016 Jonathan Wakely - 2.0.0-33.20160121git6f51b3 - Rebuilt for linker errors in boost (#1331983) * Sat Mar 12 2016 Antonio Trande - 2.0.0-32.20160121git6f51b3 - Rebuild for GLPK-4.59 * Fri Feb 19 2016 Antonio Trande - 2.0.0-31.20160121git6f51b3 - Rebuild for GLPK-4.58 * Mon Feb 15 2016 Antonio Trande - 2.0.0-30.20160121git6f51b3 - Macros removed from Obsolets tags * Sun Feb 14 2016 Antonio Trande - 2.0.0-29.20160121git6f51b3 - PyOpenMS disabled on x86 arches - Remove invalid tags from appdata files * Sun Feb 14 2016 Antonio Trande - 2.0.0-28.20160121git6f51b3 - Specified the number of Make jobs - Patched for GCC-6 * Thu Feb 04 2016 Fedora Release Engineering - 2.0.0-27.20160121git6f51b3 - Rebuilt for https://fedoraproject.org/wiki/Fedora_24_Mass_Rebuild * Wed Jan 27 2016 Antonio Trande - 2.0.0-26.20160121git6f51b3 - Fixed package dependency * Tue Jan 26 2016 Antonio Trande - 2.0.0-25.20160121git6f51b3 - Data sub-package arched * Mon Jan 25 2016 Antonio Trande - 2.0.0-24.20160121git6f51b3 - Disabled HAS_XSERVER option * Fri Jan 22 2016 Antonio Trande - 2.0.0-23.20160121git6f51b3 - Update to commit #6f51b3 - Excluded some tests - Added python provides macros - Rebuild for wildmagic5-5.14 - Fixed Python2 sub-package - Removed tutorials * Thu Dec 10 2015 Antonio Trande - 2.0.0-22.20151210gitf19f8b - Update to commit #f19f8b - Python3 binding - Added python-biopython as BR package * Wed Nov 04 2015 Antonio Trande - 2.0.0-21.20150529git88dc25 - Hardened builds on - 2.0.0-20.20150529git88dc25 - Rebuilt for Boost 1.59 * Wed Jul 29 2015 Fedora Release Engineering - 2.0.0-19.20150529git88dc25 - Rebuilt for https://fedoraproject.org/wiki/Changes/F23Boost159 * Fri Jul 24 2015 Antonio Trande 2.0.0-18.20150529git88dc25 - Rebuild again * Sat Jul 18 2015 Antonio Trande 2.0.0-17.20150529git88dc25 - Rebuild for Boost upgrade to 1.58.0 * Thu Jun 18 2015 Fedora Release Engineering - 2.0.0-16.20150529git88dc25 - Rebuilt for https://fedoraproject.org/wiki/Fedora_23_Mass_Rebuild * Fri Jun 12 2015 Antonio Trande 2.0.0-15.20150529git88dc25 - memleak test excluded again * Tue Jun 09 2015 Antonio Trande 2.0.0-14.20150529git88dc25 - Exclude TOPP_OpenSwathAssayGenerator_test_1_out1 test * Tue Jun 09 2015 Antonio Trande 2.0.0-13.20150529git88dc25 - Update to the post-release #88dc25 - Packaged MetaProSIP and OpenSwathAssayGenerator - Obsolete wrong python2-openms 2.0.0 - Replaced XTandem with fido-pi * Fri May 15 2015 Antonio Trande 2.0.0-12 - Bug fix in upstream desktop files * Fri May 15 2015 Antonio Trande 2.0.0-11 - Fix PeakPickerWavelet test - Set environment variables in desktop files * Fri May 08 2015 Antonio Trande 2.0.0-10 - Excluded TOPP_XTandemAdapter_ test * Fri May 08 2015 Antonio Trande 2.0.0-9 - Rebuild after XTandem update - Try to execute XTandem test * Sat May 02 2015 Antonio Trande 2.0.0-8 - memleaks test excluded * Sat May 02 2015 Antonio Trande 2.0.0-7 - mzML unittests patched - PyOpenMS compiled without parallel make - PyOpenMS tests disabled * Fri May 01 2015 Antonio Trande 2.0.0-6 - Source archive re-compressed by upstream - Sym-linked the library pyopenms/libSuperHirn.so * Fri May 01 2015 Antonio Trande 2.0.0-5 - SPEC cleanups * Thu Apr 30 2015 Antonio Trande 2.0.0-4 - Patched pyOpenMS version definition - Removed 'pyopenms_bdist_egg' make target * Thu Apr 30 2015 Antonio Trande 2.0.0-3 - PyOpenMS is still compiled against Python2 on Linux * Mon Apr 13 2015 Antonio Trande 2.0.0-2 - Fix make test * Sat Apr 11 2015 Antonio Trande 2.0.0-1 - Update to the release 2.0 * Mon Jan 26 2015 Petr Machata - 1.11.1-12 - Rebuild for boost 1.57.0 * Sat Dec 13 2014 Antonio Trande 1.11.1-11 - Parallel make disabled * Fri Dec 12 2014 Antonio Trande 1.11.1-10 - Parallel make just on Fedora 20+ * Mon Dec 08 2014 Antonio Trande 1.11.1-9 - Fixed unused-direct-shlib-dependency warnings - Fixed residual spurious executable permissions - Avoided python shared object stripping - Added a patch (Patch5) to detect additional QT libraries * Fri Dec 05 2014 Antonio Trande 1.11.1-8 - Fixed INIFileEditor .desktop file - Fixed some spurious executable permissions * Fri Dec 05 2014 Antonio Trande 1.11.1-7 - Fixed some cmake options - Fixed %%post/%%postun/%%posttrans - Added TOPP and Tutorial tests - Fixed iCPP warnings of the PNG files - Built a noarch data sub-package - python-openms's data file directory linked to /usr/share/OpenMS - TOPP tests disabled (some of them fail) * Tue Oct 07 2014 Antonio Trande 1.11.1-6 - Added conditional arch macro * Mon Oct 06 2014 Antonio Trande 1.11.1-5 - Included XTandem BR * Mon Sep 29 2014 Antonio Trande 1.11.1-4 - Added cmake's options for TBB - Added nested C++ templates patch (Patch4) * Mon Jun 30 2014 Antonio Trande 1.11.1-3 - Added setuptools patch - Added library patch - pyOpenMS building enabled - Performed pyOpenMS tests - Added .desktop files and related .xpm icons * Sun Jun 01 2014 Antonio Trande 1.11.1-2 - Check disabled - pyOpenMS building disabled - Added a macro for pyOpenMS * Thu May 22 2014 Antonio Trande 1.11.1-1 - First package