%global __cmake_in_source_build 1 # Default ld_as_needed flag breaks executables linkage %undefine _ld_as_needed # Tests need Python2 to be executed %global with_check 0 # Documentation needs Python2 to be built %global with_doc 0 Obsoletes: seqan2-doc < 0:2.4.0-8 Name: seqan2 Summary: C++ library of efficient algorithms and data structures Version: 2.4.0 Release: 18%{?dist} License: BSD URL: http://www.seqan.de/ Source0: https://github.com/seqan/seqan/archive/seqan-v%{version}.tar.gz#/seqan-seqan-v%{version}.tar.gz # Disable automatic stripping on no-DEVELOP seqan build systems Patch0: seqan-disable_stripping.patch # Set paths of seqan-2.pc and seqan-config.cmake Patch1: %{name}-set_config_filepath.patch # Set paths of plot.awk and ps2pswLinks.gawk files Patch2: %{name}-set_awk_installation.patch BuildRequires: make BuildRequires: qt4-devel BuildRequires: cmake, gcc-c++ BuildRequires: llvm-devel BuildRequires: bzip2-devel BuildRequires: zlib-devel BuildRequires: boost-devel BuildRequires: coin-or-lemon-devel BuildRequires: libstdc++-static BuildRequires: python3-devel ## Test %if 0%{?with_check} BuildRequires: python3-nose BuildRequires: python3-pytest BuildRequires: python3-jinja2 %endif ## Bundled files exception https://fedorahosted.org/fpc/ticket/174 Provides: bundled(gnulib) %description SeqAn (version 2.x.x) is an open source C++ library of efficient algorithms and data structures for the analysis of sequences with the focus on biological data. Our library applies a unique generic design that guarantees high performance, generality, extensibility, and integration with other libraries. As such, it contains algorithms and data structures for * string representation and their manipluation, * online and indexed string search, * efficient I/O of bioinformatics file formats, * sequence alignments, and * many, many more. %package apps Summary: SeqAn (2.x.x) applications ## Seqan apps are licenses under BSD and GPLv3+ and LGPLv3+. # # BSD (3-clauses): alf, bs_tools, fiona, fx_tools, gustaf # insegt, mason2, ngs_roi, param_chooser, rabema, razers3 # sak, sam2matrix, samcat, searchjoin, seqcons2, yara # ngs_roi, pair_align, ngs_roi. # # GPLv3+: rabema. # # LGPLv3+: dfi, insegt, micro_razers, pair_align # param_chooser, razers, razers3, rep_sep, sak # seqan_tcoffee, sgip, snp_store, splazers, stellar # tree_recon. ## # LGPLv3 gives you permission to relicense the code under GPLv3 # BSD (3-clauses) is compatible with GPLv3 # We can use a collective license: License: GPLv3+ and BSD and LGPLv3+ Requires: gawk%{?_isa} # 'seqan2' is the most recent version of 'SeqAn' Obsoletes: seqan <= 0:1.4.2 Provides: seqan = 0:%{version}-%{release} %description apps All SeqAn applications. %package headers Summary: SeqAn (2.x.x) headers only files # bzip2stream and zipstream libraries are distributed under zlib/libpng # basic/boost*.h libraries are distributed under Boost # bam_io/bam_index_bai.h is distributed under MIT # Although Boost, zlib, MIT are GPL compatible, they're all tagged anyway License: GPLv3+ and BSD and MIT and LGPLv3+ and zlib and Boost Provides: bundled(bzip2stream) Provides: bundled(zipstream) %description headers C headers files of SeqAn, including pkconfig and CMake configuration files. %package examples Summary: SeqAn (2.x.x) examples Requires: %{name}-apps%{?_isa} = %{version}-%{release} %description examples Testing files of SeqAn2's apps. %if 0%{?with_doc} %package doc Summary: SeqAn (2.x.x) documentation # 3L is licensed under MIT # Less and bootstrap files is licensed under ASL 2.0 # jquery-bbq are licensed under LGPLv3+ License: LGPLv3+ and MIT and ASL 2.0 BuildRequires: python3-sphinx BuildRequires: python3-sphinx_rtd_theme Requires: fontawesome-fonts-web BuildArch: noarch # https://github.com/mateuszkocz/3l Provides: bundled(3l) = 1.4.4 # http://lesscss.org/ Provides: bundled(less) = 1.3.3 # http://twbs.github.com/bootstrap Provides: bundled(bootstrap) = 3.0.0 Obsoletes: seqan-doc <= 0:1.4.2 Provides: seqan-doc = 0:%{version}-%{release} %description doc Info files of SeqAn2's apps. %endif %prep %autosetup -p0 -n seqan-seqan-v%{version} ## Remove spurious executable permissions find . -perm /755 -type f \( -name "*.cpp" -o -name "*.h" \) -exec chmod -x {} ';' ## Renamed each single license file for appID in `ls apps/ | grep -v CMakeLists`; do cp -p apps/$appID/LICENSE apps/$appID/$appID-LICENSE done cp -p apps/rabema/COPYING apps/rabema/rabema-COPYING # Unbundle font-awesome fonts rm -rf util/py_lib/seqan/dox/tpl/lib/font-awesome/* %build mkdir -p build/library && pushd build/library SEQAN_OPT_FLAGS="$RPM_OPT_FLAGS" %cmake \ -DCMAKE_CXX_FLAGS_RELEASE:STRING="$SEQAN_OPT_FLAGS -DNDEBUG" \ -DCMAKE_INSTALL_PREFIX:PATH=%{_prefix} \ -DCMAKE_INSTALL_DOCDIR:STRING=share/doc/%{name} \ -DCMAKE_INSTALL_INCLUDEDIR:PATH=include/%{name} \ -DSYSCONF_INSTALL_DIR:PATH=%{_sysconfdir} \ -DSHARE_INSTALL_PREFIX:PATH=%{_datadir} \ -DBUILD_SHARED_LIBS:BOOL=OFF \ -DCMAKE_SKIP_RPATH:BOOL=YES -DCMAKE_SKIP_INSTALL_RPATH:BOOL=YES \ -DCMAKE_VERBOSE_MAKEFILE:BOOL=TRUE \ -DSEQAN_BUILD_SYSTEM:STRING=SEQAN_RELEASE_LIBRARY \ -DSEQAN_DISABLE_VERSION_CHECK:BOOL=ON \ -DZLIB_INCLUDE_DIR:PATH=%{_includedir} -DZLIB_LIBRARY:FILEPATH=%{_libdir}/libz.so \ -DBZIP2_INCLUDE_DIR:PATH=%{_includedir} -DBZIP2_LIBRARY:FILEPATH=%{_libdir}/libbz2.so \ -DLEMON_INCLUDE_DIR:PATH=%{_includedir} -DLEMON_LIBRARY:FILEPATH=%{_libdir}/libemon.so \ -DBoost_INCLUDE_DIR:PATH=%{_includedir} -DPYTHON_EXECUTABLE:FILEPATH=%{__python3} \ -DSPHINX_EXECUTABLE:FILEPATH=%{_bindir}/sphinx-build \ -DSPHINX_MAN_OUTPUT:BOOL=ON \ -DSPHINX_TEXT_OUTPUT:BOOL=ON \ -DYARA_LARGE_CONTIGS:BOOL=OFF ../.. %make_build popd mkdir -p build/Release && pushd build/Release SEQAN_OPT_FLAGS="$RPM_OPT_FLAGS" %cmake \ -DCMAKE_CXX_FLAGS_RELEASE:STRING="$SEQAN_OPT_FLAGS -DNDEBUG" \ -DCMAKE_INSTALL_PREFIX:PATH=%{_prefix} \ -DCMAKE_INSTALL_DOCDIR:STRING=share/doc/%{name} \ -DCMAKE_INSTALL_INCLUDEDIR:PATH=include/%{name} \ -DSYSCONF_INSTALL_DIR:PATH=%{_sysconfdir} \ -DSHARE_INSTALL_PREFIX:PATH=%{_datadir} \ -DBUILD_SHARED_LIBS:BOOL=OFF \ -DCMAKE_SKIP_RPATH:BOOL=YES -DCMAKE_SKIP_INSTALL_RPATH:BOOL=YES \ -DCMAKE_VERBOSE_MAKEFILE:BOOL=TRUE \ -DSEQAN_BUILD_SYSTEM:STRING=SEQAN_RELEASE_APPS \ -DSEQAN_DISABLE_VERSION_CHECK:BOOL=ON \ -DZLIB_INCLUDE_DIR:PATH=%{_includedir} -DZLIB_LIBRARY:FILEPATH=%{_libdir}/libz.so \ -DBZIP2_INCLUDE_DIR:PATH=%{_includedir} -DBZIP2_LIBRARY:FILEPATH=%{_libdir}/libbz2.so \ -DLEMON_INCLUDE_DIR:PATH=%{_includedir} -DLEMON_LIBRARY:FILEPATH=%{_libdir}/libemon.so \ -DBoost_INCLUDE_DIR:PATH=%{_includedir} -DPYTHON_EXECUTABLE:FILEPATH=%{__python3} \ -DYARA_LARGE_CONTIGS:BOOL=OFF \ -DSPHINX_EXECUTABLE:FILEPATH=%{_bindir}/sphinx-build \ -DSPHINX_MAN_OUTPUT:BOOL=ON \ -DSPHINX_TEXT_OUTPUT:BOOL=ON ../.. # Disable parallel Make jobs to prevent compiler errors make -O -j1 %install %make_install -C build/library %make_install -C build/Release # Unbundle font-awesome fonts %if 0%{?with_doc} ln -s %{_datadir}/font-awesome/scss %{buildroot}%{_pkgdocdir}/html/lib/font-awesome/scss ln -s %{_datadir}/font-awesome/css %{buildroot}%{_pkgdocdir}/html/lib/font-awesome/css ln -s %{_datadir}/font-awesome/fonts %{buildroot}%{_pkgdocdir}/html/lib/font-awesome/fonts ln -s %{_datadir}/font-awesome/less %{buildroot}%{_pkgdocdir}/html/lib/font-awesome/less %endif ## Fix executable permissions chmod a+x %{buildroot}%{_bindir}/* # Set permissions and make symlinks of plot.awk and ps2pswLinks.gawk files ln -s %{_datadir}/%{name}/pdf_plot_helper/plot.awk %{buildroot}%{_bindir}/plot.awk ln -s %{_datadir}/%{name}/pdf_plot_helper/ps2pswLinks.gawk %{buildroot}%{_bindir}/ps2pswLinks.gawk ## Remove unnecessary files rm -rf %{buildroot}%{_libexecdir}/seqan2/examples/ngs_roi/R rm -f %{buildroot}%{_datadir}/doc/seqan2/LICENSE rm -f %{buildroot}%{_datadir}/doc/seqan2/CHANGELOG.rst rm -f %{buildroot}%{_datadir}/doc/seqan2/README.rst %if 0%{?with_check} %check pushd build/Release ctest --force-new-ctest-process -VV --parallel %{?_smp_mflags} -E app_test_fiona %endif %files apps %license LICENSE %license apps/*/*-LICENSE apps/rabema/rabema-COPYING %doc README.rst CHANGELOG.rst %{_bindir}/* %{_mandir}/man1/* %dir %{_datadir}/%{name} %dir %{_datadir}/%{name}/pdf_plot_helper %defattr(0444, root, root) %{_datadir}/%{name}/pdf_plot_helper/plot.awk %{_datadir}/%{name}/pdf_plot_helper/ps2pswLinks.gawk %files headers %license include/seqan/LICENSE %doc README.rst CHANGELOG.rst %{_includedir}/%{name}/ %{_libdir}/cmake/%{name}/ %{_libdir}/pkgconfig/seqan-2.pc %files examples %{_libexecdir}/%{name}/ %exclude %{_libexecdir}/%{name}/examples/*/LICENSE %if 0%{?with_doc} %files doc %license LICENSE %doc README.rst CHANGELOG.rst %{_pkgdocdir}/ %endif %changelog * Sat Jul 23 2022 Fedora Release Engineering - 2.4.0-18 - Rebuilt for https://fedoraproject.org/wiki/Fedora_37_Mass_Rebuild * Sun Jul 10 2022 Antonio Trande - 2.4.0-17 - Drop Java dependency (rhbz#2104101) * Sat Feb 05 2022 Jiri Vanek - 2.4.0-16 - Rebuilt for java-17-openjdk as system jdk * Sat Jan 22 2022 Fedora Release Engineering - 2.4.0-15 - Rebuilt for https://fedoraproject.org/wiki/Fedora_36_Mass_Rebuild * Fri Jul 23 2021 Fedora Release Engineering - 2.4.0-14 - Rebuilt for https://fedoraproject.org/wiki/Fedora_35_Mass_Rebuild * Tue Mar 30 2021 Jonathan Wakely - 2.4.0-13 - Rebuilt for removed libstdc++ symbol (#1937698) * Wed Jan 27 2021 Fedora Release Engineering - 2.4.0-12 - Rebuilt for https://fedoraproject.org/wiki/Fedora_34_Mass_Rebuild * Sat Aug 01 2020 Fedora Release Engineering - 2.4.0-11 - Second attempt - Rebuilt for https://fedoraproject.org/wiki/Fedora_33_Mass_Rebuild * Wed Jul 29 2020 Fedora Release Engineering - 2.4.0-10 - Rebuilt for https://fedoraproject.org/wiki/Fedora_33_Mass_Rebuild * Thu Jan 30 2020 Fedora Release Engineering - 2.4.0-9 - Rebuilt for https://fedoraproject.org/wiki/Fedora_32_Mass_Rebuild * Fri Nov 15 2019 Antonio Trande - 2.4.0-8 - Switch to Python3 - Disable documentation build - Disable check * Sat Feb 02 2019 Fedora Release Engineering - 2.4.0-7 - Rebuilt for https://fedoraproject.org/wiki/Fedora_30_Mass_Rebuild * Mon Oct 15 2018 Miro Hrončok - 2.4.0-6 - Remove build dependency on python2-sphinxcontrib-bibtex * Sun Oct 07 2018 Antonio Trande - 2.4.0-5 - Undefine ld_as_needed flag * Sat Jul 14 2018 Fedora Release Engineering - 2.4.0-4 - Rebuilt for https://fedoraproject.org/wiki/Fedora_29_Mass_Rebuild * Wed Mar 07 2018 Adam Williamson - 2.4.0-3 - Rebuild to fix GCC 8 mis-compilation See https://da.gd/YJVwk ("GCC 8 ABI change on x86_64") * Fri Feb 09 2018 Fedora Release Engineering - 2.4.0-2 - Rebuilt for https://fedoraproject.org/wiki/Fedora_28_Mass_Rebuild * Fri Feb 02 2018 Antonio Trande - 2.4.0-1 - Update to version 2.4.0 * Wed Jan 17 2018 Antonio Trande - 2.4.0-0.4.20180103git8a875d - Fix dependencies * Tue Jan 16 2018 Antonio Trande - 2.4.0-0.3.20180103git8a875d - Split off applications in a single sub-package - Devel rpm renamed seqan-headers * Sat Jan 13 2018 Antonio Trande - 2.4.0-0.2.20180103git8a875d - plot.awk/ps2pswLinks.gawk installed in a private share datadir - plot.awk/ps2pswLinks.gawk symliked in '_bindir' - Renamed each single license file * Wed Jan 10 2018 Antonio Trande - 2.4.0-0.1.20180103git8a875d - Pre-released as seqan-2.4.0 - Add gcc-c++ BR - Remove unnecessary R files - Unbundle font-awesome - Apps/libraries licensing commented * Mon Jan 08 2018 Antonio Trande - 2.3.2-3.20180103git8a875d - Documentation still disabled * Wed Jan 03 2018 Antonio Trande - 2.3.2-2.20180103git8a875d - Build devel commit #8a875d - Add manually -DNDEBUG flag * Wed Sep 20 2017 Antonio Trande - 2.3.2-1 - Update to 2.3.2 * Thu Aug 03 2017 Fedora Release Engineering - 1.4.2-33 - Rebuilt for https://fedoraproject.org/wiki/Fedora_27_Binutils_Mass_Rebuild * Sun Jul 30 2017 Florian Weimer - 1.4.2-32 - Rebuild with binutils fix for ppc64le (#1475636) * Thu Jul 27 2017 Fedora Release Engineering - 1.4.2-31 - Rebuilt for https://fedoraproject.org/wiki/Fedora_27_Mass_Rebuild * Tue Jul 04 2017 Jonathan Wakely - 1.4.2-30 - Rebuilt for Boost 1.64 * Mon May 15 2017 Fedora Release Engineering - 1.4.2-29 - Rebuilt for https://fedoraproject.org/wiki/Fedora_26_27_Mass_Rebuild * Sat Feb 11 2017 Fedora Release Engineering - 1.4.2-28 - Rebuilt for https://fedoraproject.org/wiki/Fedora_26_Mass_Rebuild * Fri Jan 27 2017 Jonathan Wakely - 1.4.2-27 - Rebuilt for Boost 1.63 * Sat Nov 12 2016 Antonio Trande - 1.4.2-26 - Skip tests on s390 and ppc * Sat Nov 12 2016 Antonio Trande - 1.4.2-25 - Skip failed tests * Sat Feb 20 2016 Antonio Trande - 1.4.2-24 - Fixed compiler/linker flags * Thu Feb 04 2016 Fedora Release Engineering - 1.4.2-23 - Rebuilt for https://fedoraproject.org/wiki/Fedora_24_Mass_Rebuild * Fri Jan 15 2016 Jonathan Wakely - 1.4.2-22 - Rebuilt for Boost 1.60 * Wed Oct 21 2015 Antonio Trande - 1.4.2-21 - Actived hardened build * Tue Oct 13 2015 Antonio Trande - 1.4.2-20 - Rebuilt for cmake 3.4.0 - Used %%license * Thu Aug 27 2015 Jonathan Wakely - 1.4.2-19 - Rebuilt for Boost 1.59 * Wed Jul 29 2015 Fedora Release Engineering - 1.4.2-18 - Rebuilt for https://fedoraproject.org/wiki/Changes/F23Boost159 * Sat Jul 18 2015 Antonio Trande - 1.4.2-17 - Parallel make always disabled * Sat Jul 18 2015 Antonio Trande - 1.4.2-16 - Rebuild for Boost upgrade to 1.58.0 * Fri Jun 19 2015 Fedora Release Engineering - 1.4.2-15 - Rebuilt for https://fedoraproject.org/wiki/Fedora_23_Mass_Rebuild * Fri May 15 2015 Antonio Trande - 1.4.2-14 - Reduce optimization to -O0 (cc1plus error persists) * Fri May 15 2015 Antonio Trande - 1.4.2-13 - SPEC cleanups * Fri May 15 2015 Antonio Trande - 1.4.2-12 - Removed -pipe flag because of cc1plus error on ARMs * Thu May 14 2015 Antonio Trande - 1.4.2-11 - Set job=1 to Make on ARMs aarch64 ppc64 ppc64le * Thu May 14 2015 Antonio Trande - 1.4.2-10 - Downgrading to 1.4.2 - Excluded s390 s390x arches - Excluded bstools_test on ARMs aarch64 ppc64 ppc64le * Mon Jan 26 2015 Petr Machata - 1.4.2-9 - Rebuild for boost 1.57.0 * Tue Dec 02 2014 Antonio Trande - 1.4.2-8 - Excluded bs_tools test on ARM * Mon Dec 01 2014 Antonio Trande - 1.4.2-7 - Parallel tests not performed on ARM * Mon Dec 01 2014 Antonio Trande - 1.4.2-6 - DBUILD_SHARED_LIBS boolean disabled - Test enabled * Tue Nov 25 2014 Antonio Trande - 1.4.2-5 - Parallel make excluded on ARM arch * Tue Nov 25 2014 Antonio Trande - 1.4.2-4 - Tests disabled temporarily * Sat Nov 22 2014 Antonio Trande - 1.4.2-3 - Packaged private libraries - Performed tests - Splazers and fiona tests excluded * Sat Nov 22 2014 Antonio Trande - 1.4.2-2 - Parallel make excluded on ARM arch * Fri Nov 21 2014 Antonio Trande - 1.4.2-1 - Update to 1.4.2 - Fixed cmake compiler flags - Fixed declaration of multiple license - A doc sub-package is now built * Mon Aug 18 2014 Fedora Release Engineering - 1.4.1-3 - Rebuilt for https://fedoraproject.org/wiki/Fedora_21_22_Mass_Rebuild * Sat Jun 14 2014 Antonio Trande 1.4.1-2 - Added 'Provides:bundled(gnulib)' - Changed find command for executable permissions fixing - Use %%make_install - Fixed wrong-file-end-of-line-encoding warnings * Wed Jun 11 2014 Antonio Trande 1.4.1-1 - First package