## START: Set by rpmautospec ## (rpmautospec version 0.8.1) ## RPMAUTOSPEC: autorelease, autochangelog %define autorelease(e:s:pb:n) %{?-p:0.}%{lua: release_number = 1; 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 Name: percolator Summary: Software for postprocessing of shotgun proteomics data Version: 3.08 Release: %autorelease ## Code under src/ (except RAMP) is licensed under a ASL 2.0 license. ## Code under src/converters/MSToolkit/RAMP is licensed under a LGPLv2+ license. License: Apache-2.0 AND LGPL-2.0-or-later URL: https://github.com/percolator/percolator Source0: https://github.com/percolator/percolator/archive/rel-3-08/percolator-rel-3-08.tar.gz BuildRequires: make BuildRequires: gcc, gcc-c++ BuildRequires: cmake # Needed for testing BuildRequires: gtest-devel BuildRequires: eigen3-devel BuildRequires: python3-devel BuildRequires: boost-static, boost-devel BuildRequires: pkgconfig(tokyocabinet) BuildRequires: pkgconfig(xerces-c) BuildRequires: pkgconfig(sqlite3) BuildRequires: pkgconfig(libtirpc) BuildRequires: xsd, zlib-devel, bzip2-devel Patch0: percolator-unbundle_eigen_gtest.patch Requires: %{name}-data = %{version}-%{release} Obsoletes: fido-pi = 0:0 %description The first step in analyzing an mass spectrometry assay is to match the harvested spectra against a target database using database search engines such as Sequest and Mascot, a process that renders list of peptide-spectrum matches. However, it is not trivial to assess the accuracy of these identifications. Percolator uses a semi-supervised machine learning to discriminate correct from incorrect peptide-spectrum matches, and calculates accurate statistics such as q-value (FDR) and posterior error probabilities. %package data Summary: percolator data files BuildArch: noarch Requires: xml-common %description data This package contains XSD data files of %{name} and models of elude tool. %package static Summary: percolator static libraries %description static This package contains static libraries of %{name}. %prep %autosetup -n percolator-rel-3-08 -N %patch -P 0 -p1 -b .backup ## Remove spurious executable permissions find . -type f -name "*.cpp" -exec chmod 0644 '{}' \; find . -type f -name "*.h" -exec chmod 0644 '{}' \; find . -type f -name "*.xx" -exec chmod 0644 '{}' \; find . -type f -name "*.txt" -exec chmod 0644 '{}' \; # Remove bundled files rm -rf percolator/_deps/* ## Rename additional readme files chmod a-x src/converters/MSToolkit/RAMP/README mv src/converters/MSToolkit/RAMP/README src/converters/MSToolkit/RAMP/RAMP-README mv src/converters/MSToolkit/RAMP/Readme.Mike.txt src/converters/MSToolkit/RAMP/RAMP-Readme.Mike.txt ## Set 'qvality' destination directory sed -e 's|./bin|bin|g' -i src/qvality/CMakeLists.txt %build export CXXFLAGS="-std=c++14 $RPM_OPT_FLAGS" mkdir -p percolator %cmake -Wno-dev -B percolator -S ./ \ -DCMAKE_COLOR_MAKEFILE:BOOL=ON \ -DCMAKE_VERBOSE_MAKEFILE=TRUE -DXML_SUPPORT:BOOL=ON \ -DCMAKE_CXX_FLAGS_RELEASE:STRING="%{optflags} -Isrc -I%{_includedir}/xsd/cxx/tree -I%{_includedir}/tirpc -I%{_includedir}/eigen3" \ -DCMAKE_EXE_LINKER_FLAGS_RELEASE:STRING="%{__global_ldflags} -ltirpc" \ -DCMAKE_BUILD_TYPE:STRING=Release -DBUILD_TESTING:BOOL=ON \ -DCMAKE_SKIP_INSTALL_RPATH:BOOL=YES -DCMAKE_SKIP_RPATH:BOOL=YES \ -DTARGET_ARCH=%{_arch} ### XSD files ran maually ### In Fedora 'xsd' executable is 'xsdcxx' xsdcxx cxx-tree --generate-insertion XDR --generate-extraction XDR --root-element-all \ --namespace-map http://per-colator.com/percolator_in/13=percolatorInNs src/xml/percolator_in.xsd xsdcxx cxx-tree --generate-serialization --generate-insertion XDR --generate-extraction XDR --root-element-all \ --namespace-map http://per-colator.com/percolator_out/15=percolatorOutNs src/xml/percolator_out.xsd ### %define _vpath_builddir percolator %cmake_build mkdir -p src/fido %cmake -Wno-dev -B src/fido \ -DCMAKE_COLOR_MAKEFILE:BOOL=ON \ -DCMAKE_VERBOSE_MAKEFILE=TRUE \ -DCMAKE_BUILD_TYPE:STRING=Release \ -DTokyoCabinet_INCLUDE_DIR=%{_includedir} \ -DTokyoCabinet_LIBRARY=%{_libdir}/libtokyocabinet.so \ -DCMAKE_CXX_FLAGS_RELEASE:STRING="%{optflags} -Isrc -I%{_includedir}/xsd/cxx/tree -I%{_includedir}/tirpc -I%{_includedir}/eigen3" \ -DCMAKE_EXE_LINKER_FLAGS_RELEASE:STRING="%{__global_ldflags} -ltirpc" \ -DCMAKE_SKIP_INSTALL_RPATH:BOOL=YES -DCMAKE_SKIP_RPATH:BOOL=YES \ -DTARGET_ARCH=%{_arch} -DBUILD_TESTING:BOOL=ON %define _vpath_builddir src/fido %cmake_build mkdir -p src/converters %cmake -Wno-dev -B src/converters \ -DCMAKE_COLOR_MAKEFILE:BOOL=ON \ -DCMAKE_VERBOSE_MAKEFILE=TRUE \ -DCMAKE_CXX_FLAGS_RELEASE:STRING="%{optflags} -Isrc -I%{_includedir}/xsd/cxx/tree -I%{_includedir}/tirpc -I%{_includedir}/eigen3" \ -DCMAKE_EXE_LINKER_FLAGS_RELEASE:STRING="%{__global_ldflags} -ltirpc" \ -DCMAKE_BUILD_TYPE:STRING=Release \ -DPERCOLATOR-CONVERTERS_BINARY_DIR:STATIC=converters \ -DCMAKE_SKIP_INSTALL_RPATH:BOOL=YES -DCMAKE_SKIP_RPATH:BOOL=YES \ -DTokyoCabinet_INCLUDE_DIR=%{_includedir} \ -DTokyoCabinet_LIBRARY=%{_libdir}/libtokyocabinet.so \ -DSERIALIZE="TokyoCabinet" \ -DTARGET_ARCH=%{_arch} -DBUILD_TESTING:BOOL=ON ### XSD files ran maually ### In Fedora 'xsd' executable is 'xsdcxx' xsdcxx cxx-tree --generate-serialization --generate-insertion XDR --generate-extraction XDR --root-element-all \ --namespace-map http://per-colator.com/percolator_in/13=percolatorInNs src/xml/percolator_in.xsd xsdcxx cxx-tree --generate-serialization --generate-insertion XDR --generate-extraction XDR --root-element-all \ --namespace-map http://per-colator.com/percolator_out/15=percolatorOutNs src/xml/percolator_out.xsd ## xsdcxx cxx-tree --generate-serialization --generate-insertion XDR --generate-extraction XDR --root-element-all \ --namespace-map http://psidev.info/psi/pi/mzIdentML/1.1=mzIdentML_ns src/xml/mzIdentML1.1.0.xsd xsdcxx cxx-tree --generate-serialization --generate-insertion XDR --generate-extraction XDR --root-element-all \ --namespace-map http://www.bioml.com/gaml/=gaml_tandem_ns src/xml/gaml_tandem1.0.xsd xsdcxx cxx-tree --generate-serialization --generate-insertion XDR --generate-extraction XDR --root-element-all \ --namespace-map http://www.thegpm.org/TANDEM/2011.12.01.1=tandem_ns --namespace-map =tandem_ns \ --namespace-map http://www.bioml.com/gaml/=gaml_tandem_ns src/xml/tandem2011.12.01.1.xsd ### %define _vpath_builddir src/converters %cmake_build %install %define _vpath_builddir percolator %cmake_install %define _vpath_builddir src/converters %cmake_install ## Install static libraries mkdir -p %{buildroot}%{_libdir}/percolator for i in `find . -type f \( -name "*.a" \)`; do install -pm 755 $i %{buildroot}%{_libdir}/percolator done rm -f %{buildroot}%{_bindir}/gtest_unit %check %define _vpath_builddir percolator # https://github.com/percolator/percolator/issues/354 %ifarch %{ix86} # nothing %else %ctest -VV %endif %files %{_bindir}/percolator %{_bindir}/qvality %files data %doc ReadMe.txt %doc src/converters/MSToolkit/RAMP/RAMP-* %license license.txt %{_datadir}/xml/percolator/ %files static %doc ReadMe.txt %doc src/converters/MSToolkit/RAMP/RAMP-* %license license.txt %{_libdir}/percolator/ %changelog ## START: Generated by rpmautospec * Wed Jul 23 2025 Antonio Trande - 3.08-1 - Release 3.08 (rhbz#2381357) * Fri Jan 17 2025 Fedora Release Engineering - 3.06.04-6 - Rebuilt for https://fedoraproject.org/wiki/Fedora_42_Mass_Rebuild * Fri Oct 18 2024 Pete Walter - 3.06.04-5 - Rebuild for xerces-c 3.3 * Thu Jul 18 2024 Fedora Release Engineering - 3.06.04-4 - Rebuilt for https://fedoraproject.org/wiki/Fedora_41_Mass_Rebuild * Thu Jan 25 2024 Fedora Release Engineering - 3.06.04-3 - Rebuilt for https://fedoraproject.org/wiki/Fedora_40_Mass_Rebuild * Sun Jan 21 2024 Fedora Release Engineering - 3.06.04-2 - Rebuilt for https://fedoraproject.org/wiki/Fedora_40_Mass_Rebuild * Fri Dec 08 2023 Antonio Trande - 3.06.04-1 - Release 3.06.04 * Sun Dec 03 2023 Antonio Trande - 3.06.03-2 - Fix name of main directory * Sun Dec 03 2023 Antonio Trande - 3.06.03-1 - Release 3.06.03 * Sun Nov 19 2023 Antonio Trande - 3.06.02-1 - Release 3.06.02 * Thu Jul 20 2023 Fedora Release Engineering - 3.06.01-6 - Rebuilt for https://fedoraproject.org/wiki/Fedora_39_Mass_Rebuild * Sun Jul 02 2023 Antonio Trande - 3.06.01-5 - Exclude tests on i686 * Sun Jul 02 2023 Antonio Trande - 3.06.01-4 - Exclude some tests on i686 * Sat Jun 17 2023 Antonio Trande - 3.06.01-3 - Remove converters tests * Thu Jun 15 2023 Antonio Trande - 3.06.01-2 - Fix tests * Thu Jun 15 2023 Antonio Trande - 3.06.01-1 - Release 3.06.01| Elude support dropped * Thu Jan 19 2023 Fedora Release Engineering - 3.05-14 - Rebuilt for https://fedoraproject.org/wiki/Fedora_38_Mass_Rebuild * Fri Jul 22 2022 Fedora Release Engineering - 3.05-13 - Rebuilt for https://fedoraproject.org/wiki/Fedora_37_Mass_Rebuild * Thu Jan 20 2022 Fedora Release Engineering - 3.05-12 - Rebuilt for https://fedoraproject.org/wiki/Fedora_36_Mass_Rebuild * Thu Jul 22 2021 Fedora Release Engineering - 3.05-11 - Rebuilt for https://fedoraproject.org/wiki/Fedora_35_Mass_Rebuild * Tue Feb 16 2021 Antonio T - 3.05-10 - Undo latest file deletion * Tue Feb 16 2021 Antonio T - 3.05-9 - Obsolete fido-pi (Fedora 34+) * Tue Jan 26 2021 Fedora Release Engineering - 3.05-8 - Rebuilt for https://fedoraproject.org/wiki/Fedora_34_Mass_Rebuild * Fri Jan 08 2021 Tom Stellard - 3.05-7 - Add BuildRequires: make * Wed Aug 19 2020 Jeff Law - 3.05-6 - Force C++14 as this code is not C++17 ready * Tue Aug 04 2020 sagitter - 3.05-5 - Enable __cmake_in_source_build * Sat Aug 01 2020 Fedora Release Engineering - 3.05-4 - Second attempt - Rebuilt for https://fedoraproject.org/wiki/Fedora_33_Mass_Rebuild * Tue Jul 28 2020 Fedora Release Engineering - 3.05-3 - Rebuilt for https://fedoraproject.org/wiki/Fedora_33_Mass_Rebuild * Tue May 19 2020 sagitter - 3.05-2 - Fix EPEL7 builds (use boost169) * Tue May 19 2020 sagitter - 3.05-1 - Release 3.05 * Wed Jan 29 2020 Fedora Release Engineering - 3.04-2 - Rebuilt for https://fedoraproject.org/wiki/Fedora_32_Mass_Rebuild * Sat Sep 21 2019 sagitter - 3.04-1 - Release 3.04 * Thu Jul 25 2019 sagitter - 3.03-1 - Release 3.03 * Fri Feb 01 2019 Fedora Release Engineering - 3.02.01-3 - Rebuilt for https://fedoraproject.org/wiki/Fedora_30_Mass_Rebuild * Mon Jan 28 2019 Igor Gnatenko - 3.02.01-2 - Fix RHEL conditions * Sat Nov 03 2018 sagitter - 3.02.01-1 - Release 3.02.01 * Fri Jul 13 2018 Fedora Release Engineering - 3.02.00-7 - Rebuilt for https://fedoraproject.org/wiki/Fedora_29_Mass_Rebuild * Thu Feb 22 2018 sagitter - 3.02.00-6 - Add gcc gcc-c++ BR * Sat Feb 17 2018 sagitter - 3.02.00-5 - Link to libtirpc on fedora only * Sat Feb 17 2018 sagitter - 3.02.00-4 - Link to libtirpc * Thu Feb 15 2018 sagitter - 3.02.00-3 - Add tirpc cflag manually * Thu Feb 15 2018 sagitter - 3.02.00-2 - Add libtirpc BR * Thu Feb 15 2018 sagitter - 3.02.00-1 - Update to 3.02.0 * Thu Feb 08 2018 Fedora Release Engineering - 3.01.02-2 - Rebuilt for https://fedoraproject.org/wiki/Fedora_28_Mass_Rebuild * Sun Oct 15 2017 sagitter - 3.01.02-1 - Update to 3.01.02 * Thu Aug 03 2017 Fedora Release Engineering - 3.01-6 - Rebuilt for https://fedoraproject.org/wiki/Fedora_27_Binutils_Mass_Rebuild * Thu Jul 27 2017 Fedora Release Engineering - 3.01-5 - Rebuilt for https://fedoraproject.org/wiki/Fedora_27_Mass_Rebuild * Sat Jul 08 2017 sagitter - 3.01-4 - URL changed to GitHub * Sat Feb 11 2017 Fedora Release Engineering - 3.01-3 - Rebuilt for https://fedoraproject.org/wiki/Fedora_26_Mass_Rebuild * Wed Feb 01 2017 Jonathan Wakely - 3.01-2 - Rebuilt for Boost 1.63 and patched for GCC 7 * Thu Nov 17 2016 sagitter - 3.01-1 - Update to 3.01 * Thu Jun 09 2016 sagitter - 3.0-1 - Update to 3.0 * Mon Feb 15 2016 sagitter - 2.10.1-10 - Fixed cflags to Boost148 (EPEL) * Fri Feb 05 2016 sagitter - 2.10.1-9 - Update to commit #a4d14b * Thu Feb 04 2016 Fedora Release Engineering - 2.10.1-8 - Rebuilt for https://fedoraproject.org/wiki/Fedora_24_Mass_Rebuild * Fri Jan 15 2016 Jonathan Wakely - 2.10.1-7 - Rebuilt for Boost 1.60 * Wed Dec 23 2015 sagitter - 2.10.1-6 - Used always 'cmake' command * Sat Nov 14 2015 sagitter - 2.10.1-5 - Packaging upgrade for EPEL * Thu Aug 27 2015 Jonathan Wakely - 2.10.1-4 - Rebuilt for Boost 1.59 * Wed Jul 29 2015 Dennis Gilmore - 2.10.1-3 - Rebuilt for https://fedoraproject.org/wiki/Changes/F23Boost159 * Sat Jul 18 2015 sagitter - 2.10.1-2 - Rebuild for Boost upgrade to 1.58.0 * Wed Jul 08 2015 sagitter - 2.10.1-1 - Update to 2.10.1 * Thu Jun 18 2015 Dennis Gilmore - 2.09.0-2 - Rebuilt for https://fedoraproject.org/wiki/Fedora_23_Mass_Rebuild * Mon May 25 2015 sagitter - 2.09.0-1 - New package (bz#1224385) ## END: Generated by rpmautospec