%undefine _ld_as_needed %global __cmake_in_source_build 1 Name: percolator Summary: Software for postprocessing of shotgun proteomics data Version: 3.06.04 Release: 5%{?dist} ## 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-3-06-04/percolator-rel-3-06-04.tar.gz ## Example files for testing ## https://github.com/percolator/percolator/wiki/Example Source1: http://noble.gs.washington.edu/proj/percolator/data/yeast-01.sqt.tar.gz Source2: %{name}-RAMP_license_lgpl-2.1.txt BuildRequires: make BuildRequires: gcc, gcc-c++ BuildRequires: cmake # Needed for testing BuildRequires: gtest-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 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-3-06-04 tar -xvf %{SOURCE1} ## 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 '{}' \; ## 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 ## Included LGPLv2+ license cp -p %{SOURCE2} RAMP_license_lgpl-2.1.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 && pushd percolator %cmake -Wno-dev \ -DCMAKE_COLOR_MAKEFILE:BOOL=ON \ -DCMAKE_VERBOSE_MAKEFILE=TRUE -DXML_SUPPORT:BOOL=ON \ -DCMAKE_CXX_FLAGS_RELEASE:STRING="%{optflags} -I../src -I%{_includedir}/xsd/cxx/tree -I%{_includedir}/tirpc" \ -DCMAKE_EXE_LINKER_FLAGS_RELEASE:STRING="%{__global_ldflags} -ltirpc" \ -DCMAKE_BUILD_TYPE:STRING=Release \ -DCMAKE_SKIP_INSTALL_RPATH:BOOL=YES -DCMAKE_SKIP_RPATH:BOOL=YES \ -DTARGET_ARCH=%{_arch} .. ### XSD files ran maually ### In Fedora 'xsd' executable is 'xsdcxx' cd src 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 cd .. ### %make_build popd mkdir -p fido && pushd fido %cmake -Wno-dev \ -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} -I../src -I%{_includedir}/xsd/cxx/tree -I%{_includedir}/tirpc" \ -DCMAKE_EXE_LINKER_FLAGS_RELEASE:STRING="%{__global_ldflags} -ltirpc" \ -DCMAKE_SKIP_INSTALL_RPATH:BOOL=YES -DCMAKE_SKIP_RPATH:BOOL=YES \ -DTARGET_ARCH=%{_arch} ../src/fido %make_build popd mkdir -p converters && pushd converters %cmake -Wno-dev \ -DCMAKE_COLOR_MAKEFILE:BOOL=ON \ -DCMAKE_VERBOSE_MAKEFILE=TRUE \ -DCMAKE_CXX_FLAGS_RELEASE:STRING="%{optflags} -I../src -I%{_includedir}/xsd/cxx/tree -I%{_includedir}/tirpc" \ -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} ../src/converters ### 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 ### %make_build popd %install %make_install -C percolator %make_install -C converters ## 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 mkdir -p test && pushd test ../converters/sqt2pin -o pin.tab ../yeast-01.sqt ../yeast-01.shuffled.sqt ../percolator/src/percolator -X pout.xml pin.tab > yeast-01.psms popd pushd percolator # https://github.com/percolator/percolator/issues/354 %ifarch %{ix86} #%%ctest %else %ctest %endif popd %files %{_bindir}/percolator %{_bindir}/sqt2pin %{_bindir}/qvality %{_bindir}/tandem2pin %{_bindir}/msgf2pin %files data %doc ReadMe.txt %doc src/converters/MSToolkit/RAMP/RAMP-* %license license.txt %license RAMP_license_lgpl-2.1.txt %{_datadir}/percolator/ %{_datadir}/xml/percolator/ %files static %doc ReadMe.txt %doc src/converters/MSToolkit/RAMP/RAMP-* %license license.txt %license RAMP_license_lgpl-2.1.txt %{_libdir}/percolator/ %changelog * 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 - 3.06.03-1 - Release 3.06.03 * Sun Nov 19 2023 Antonio Trande - 3.06.02-1 - Release 3.06.02 - Drop EPEL7 support * Thu Jul 20 2023 Fedora Release Engineering - 3.06.01-2 - Rebuilt for https://fedoraproject.org/wiki/Fedora_39_Mass_Rebuild * Thu Jun 15 2023 Antonio Trande - 3.06.01-1 - Release 3.06.01 - Elude support dropped * Thu Jan 19 2023 Fedora Release Engineering - 3.05-11 - Rebuilt for https://fedoraproject.org/wiki/Fedora_38_Mass_Rebuild * Fri Jul 22 2022 Fedora Release Engineering - 3.05-10 - Rebuilt for https://fedoraproject.org/wiki/Fedora_37_Mass_Rebuild * Thu Jan 20 2022 Fedora Release Engineering - 3.05-9 - Rebuilt for https://fedoraproject.org/wiki/Fedora_36_Mass_Rebuild * Thu Jul 22 2021 Fedora Release Engineering - 3.05-8 - Rebuilt for https://fedoraproject.org/wiki/Fedora_35_Mass_Rebuild * Tue Feb 16 2021 Antonio Trande - 3.05-7 - Obsolete fido-pi (Fedora 34+) * Tue Jan 26 2021 Fedora Release Engineering - 3.05-6 - Rebuilt for https://fedoraproject.org/wiki/Fedora_34_Mass_Rebuild * Wed Aug 19 2020 Jeff Law - 3.05-5 - Force C++14 as this code is not C++17 ready * 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 Antonio Trande - 3.05-2 - Fix EPEL7 builds (use boost169) * Tue May 19 2020 Antonio Trande - 3.05-1 - Release 3.05 - Drop support for EPEL6 * Wed Jan 29 2020 Fedora Release Engineering - 3.04-2 - Rebuilt for https://fedoraproject.org/wiki/Fedora_32_Mass_Rebuild * Sat Sep 21 2019 Antonio Trande - 3.04-1 - Release 3.04 * Thu Jul 25 2019 Antonio Trande - 3.03-1 - Release 3.03 * Fri Feb 01 2019 Fedora Release Engineering - 3.02.01-2 - Rebuilt for https://fedoraproject.org/wiki/Fedora_30_Mass_Rebuild * Sat Nov 03 2018 Antonio Trande - 3.02.01-1 - Release 3.02.01 * Fri Jul 13 2018 Fedora Release Engineering - 3.02.00-3 - Rebuilt for https://fedoraproject.org/wiki/Fedora_29_Mass_Rebuild * Thu Feb 22 2018 Antonio Trande - 3.02.00-2 - Add gcc gcc-c++ BR * Thu Feb 15 2018 Antonio Trande - 3.02.00-1 - Update to 3.02.0 - Drop old patches - Link to libtirpc on fedora * Sun Oct 15 2017 Antonio Trande - 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 Antonio Trande - 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 Antonio Trande - 3.01-1 - Update to 3.01 * Thu Jun 09 2016 Antonio Trande - 3.0-1 - Update to 3.0 - Use cmake3 on epel * Sun Feb 07 2016 Antonio Trande - 2.10.1-11.20160205gita4d14b - Fixed cflags to Boost148 (EPEL) * Fri Feb 05 2016 Antonio Trande - 2.10.1-10.20160205gita4d14b - Update to commit #a4d14b * Thu Feb 04 2016 Fedora Release Engineering - 2.10.1-9 - Rebuilt for https://fedoraproject.org/wiki/Fedora_24_Mass_Rebuild * Fri Jan 15 2016 Jonathan Wakely - 2.10.1-8 - Rebuilt for Boost 1.60 * Wed Dec 23 2015 Antonio Trande 2.10.1-7 - Used always 'cmake' command * Sat Nov 14 2015 Antonio Trande 2.10.1-6 - Fixed conditional OS macros for EPEL - Set compiler/linker flags for hardened builds * Thu Oct 01 2015 Antonio Trande 2.10.1-5 - Boost directories modified to build in EPEL * Sat Aug 08 2015 Antonio Trande 2.10.1-4 - SPEC modified to build in EPEL - Patch to replace all reference to xerces-c-3.1 in EPEL6 * Wed Jul 29 2015 Fedora Release Engineering - 2.10.1-3 - Rebuilt for https://fedoraproject.org/wiki/Changes/F23Boost159 * Sat Jul 18 2015 Antonio Trande 2.10.1-2 - Rebuild for Boost upgrade to 1.58.0 * Tue Jul 07 2015 Antonio Trande 2.10.1-1 - Update to 2.10.1 - Made a -static sub-package * Thu Jun 18 2015 Fedora Release Engineering - 2.09.0-5 - Rebuilt for https://fedoraproject.org/wiki/Fedora_23_Mass_Rebuild * Mon May 25 2015 Antonio Trande 2.09.0-4 - -data sub-package now requires xml-common * Sun May 24 2015 Antonio Trande 2.09.0-3 - The licensing breakdown is documented - Removed spurious executable permissions - /usr/share/xml is co-owned * Sat May 23 2015 Antonio Trande 2.09.0-2 - Added LGPLv2+ license of RAMP parser - Made a data sub-package * Fri May 22 2015 Antonio Trande 2.09.0-1 - First package