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ugene/ugene.spec
Mamoru TASAKA 4b2f439f92 update to the latest git
2026-01-12 17:10:43 +09:00

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%global use_release_branch 0
%if 0%{?use_release_branch} < 1
# master
%global gitdate 20251230
%global gitcommit 71bdfafe45ac07c04c40ee7bb90456f96b3d8bbc
# New git commit with non-free part removed using "git filter-branch"
%global gitcommit_free 0a64d3f2396f1924ef932aed51a50b221e68a88d
%else
# currently 41.0 branch
%global gitdate 20250313
%global gitcommit c0dffab5a15e01c026f80cf0a7033b08112a355f
# New git commit with non-free part using "git filter-branch"
%global gitcommit_free b0631c54cc0603a88793ed5d6ee02dec196b823e
%endif
%global shortcommit %(c=%{gitcommit}; echo ${c:0:7})
%global git_version %{gitdate}git%{shortcommit}
%global tarballdate 20260112
%global tarballtime 1631
%global use_release 0
%global use_gitbare 1
%if 0%{?use_gitbare} < 1
# force
%global use_release 1
%endif
%if 0%{?use_release} >= 1
%global GIT true
%else
%global GIT git
%endif
%global mainver 53.0
%undefine prever
%if 0%{?use_release} >= 1
%global fedoraver %{mainver}%{?prever:~%{prerpmver}}
%endif
%if 0%{?use_gitbare} >= 1
%global fedoraver %{mainver}%{?git_version:^%{git_version}}
%endif
Name: ugene
Summary: Integrated bioinformatics toolkit
Version: %{fedoraver}
Release: 1%{?dist}
#The entire source code is GPLv2+ except:
#file src/libs_3rdparty/qtbindings_core/src/qtscriptconcurrent.h which is GPLv2
#files in src/plugins_3rdparty/script_debuger/src/qtscriptdebug/ which are GPLv2
# Automatically converted from old format: GPLv2+ and GPLv2 - review is highly recommended.
License: GPL-2.0-or-later AND GPL-2.0-only
URL: http://ugene.net
%if 0%{?use_release} >= 1
#Source0: https://github.com/ugeneunipro/ugene/archive/%{mainver}.tar.gz/#/%{name}-%{mainver}.tar.gz
# Removing non-free part
Source0: %{name}-free-%{mainver}.tar.gz
# Source0 is created by # env VERSION=%%{mainver} source ./%{SOURCE1}
%endif
%if 0%{?use_gitbare} >= 1
Source0: %{name}-free-%{tarballdate}T%{tarballtime}.tar.gz
%endif
Source1: create-ugene-free-tarball.sh
Source2: create-%{name}-git-bare-tarball.sh
# This is not installed
Source10: ugene.wrapper
Patch1: ugene-49.1-narrowing-for-unsigned-char.patch
Patch3: ugene-52.1.x-QObject-connect-overload.patch
# Currently distro-specific
Patch102: ugene-44.x-libs_3rdparty-breakpad-sys_mmap_use_system_mmap.patch
Patch103: ugene-40.1-libs_3rdparty-breakpad-unwind-nonsupported-arch.patch
Patch104: ugene-47.x-plugins_3rdparty-hmm2-nosse-arch.patch
Patch105: ugene-40.1-libs_3rdparty-breakpad-arch-port.patch
Patch106: ugene-47.x-git-plgins-smith_waterman-nonsse2-arch.patch
Patch107: ugene-40.1-qbswap-bigendian-workaround.patch
Patch109: ugene-50.x-aarch64-neon-impl-not-yet.patch
Patch110: ugene-52.x-s390x-platform-macro.patch
BuildRequires: make
BuildRequires: gcc-c++
BuildRequires: desktop-file-utils
%if 0%{?use_gitbare} >= 1
BuildRequires: %{_bindir}/git
%endif
BuildRequires: cmake(Qt5Core)
BuildRequires: cmake(Qt5Gui)
BuildRequires: cmake(Qt5LinguistTools)
BuildRequires: cmake(Qt5Network)
BuildRequires: cmake(Qt5NetworkAuth)
BuildRequires: cmake(Qt5PrintSupport)
BuildRequires: cmake(Qt5Script)
BuildRequires: cmake(Qt5ScriptTools)
BuildRequires: cmake(Qt5Sql)
BuildRequires: cmake(Qt5Svg)
BuildRequires: cmake(Qt5Test)
BuildRequires: cmake(Qt5WebSockets)
BuildRequires: cmake(Qt5Widgets)
BuildRequires: cmake(Qt5Xml)
BuildRequires: pkgconfig(gl)
BuildRequires: pkgconfig(glu)
BuildRequires: pkgconfig(sqlite3)
BuildRequires: pkgconfig(xtst)
BuildRequires: pkgconfig(zlib)
Provides: bundled(samtools) = 0.1.18
%description
Unipro UGENE is a cross-platform visual environment for DNA and protein
sequence analysis. UGENE integrates the most important bioinformatics
computational algorithms and provides an easy-to-use GUI for performing
complex analysis of the genomic data. One of the main features of UGENE
is a designer for custom bioinformatics workflows.
%prep
%if 0%{?use_release} >= 1
%setup -q
%endif
%if 0%{?use_gitbare} >= 1
%setup -q -c -n %{name}-%{mainver}%{?git_version:-%{git_version}} -T -a 0
git clone ./%{name}.git/
cd %{name}
cp -a [A-Z]* ..
git checkout -b %{mainver}-fedora %{gitcommit_free}
git config user.name "%{name} Fedora maintainer"
git config user.email "%{name}-maintainers@fedoraproject.org"
%endif
%patch -P1 -p1 -b .narrow
%GIT commit -m "Fix narrowing on arch where default char is unsigned" -a
%patch -P3 -p1 -b .include
%GIT commit -m "RegionSelectorController: specify overloaded function" -a
%patch -P102 -p1 -b .sys_mmap -Z
%GIT commit -m "libs_3rdparty/breakpad: use C function instead of directly using syscall assemble code" -a
%patch -P103 -p1 -b .unwind -Z
%GIT commit -m "libs_3rdparty/breakpad: workaround for arch not supporting unwind" -a
%patch -P104 -p1 -b .sse -Z
%GIT commit -m "plugins_3rdparty/hmm2: support architecture not supporting SSE2" -a
%patch -P105 -p1 -b .port -Z
%GIT commit -m "libs_3rdparty/breakpad: workaround for arch not ported by the upstream" -a
%patch -P106 -p1 -b .sse_2 -Z
%GIT commit -m "plugins/smith_waterman: support architecture not supporting SSE2" -a
%patch -P107 -p1 -b .char_bigen -Z
%GIT commit -m "src/corelibs/U2Core et al.: Workaround for Qt qbswap issue on Q_BIG_ENDIAN" -a
%if 1
%patch -P109 -p1 -b .neon -Z
%GIT commit -m "neon impl not yet available" -a
%endif
%patch -P110 -p1 -b .s390x_macro -Z
%GIT commit -m "define s390x related macro" -a
# Kill system-provided 3rd-party libs
sed -i CMakeLists.txt \
-e '\@add_subdirectory.*libs_3rdparty/sqlite3@d' \
-e '\@add_subdirectory.*libs_3rdparty/zlib@d' \
%{nil}
rm -rf src/libs_3rdparty/{sqlite3,zlib}
rm -rf src/include/3rdparty/{sqlite3,zlib}
%GIT rm -r -f src/libs_3rdparty/{sqlite3,zlib} || true
%GIT rm -r -f src/include/3rdparty/{sqlite3,zlib} || true
%GIT commit -m "kill system-provided 3rd-party libs" -a
grep -rl --exclude-dir=.git 3rdparty/zlib/zlib.h . | \
xargs sed -i 's|3rdparty/zlib/zlib.h|zlib.h|'
grep -rl --exclude-dir=.git 3rdparty/sqlite3/sqlite3.h . | \
xargs sed -i 's|3rdparty/sqlite3/sqlite3.h|sqlite3.h|'
find . -name CMakeLists.txt | \
xargs sed -i \
-e 's|zlib|z|' \
-e 's|ugenedb|sqlite3|' \
%{nil}
%GIT commit -m "fix system provided header path" -a
sed -i.nonfree CMakeLists.txt -e '\@add_subdirectory.*plugins_3rdparty/psipred@d'
%GIT commit -m "remove nonfree code" -a
# Remove -Werror
sed -i CMakeLists.txt -e '\@" -Werror=@d'
%GIT commit -m "remove -Werror" -a
# Enable some deprecated API
sed -i CMakeLists.txt -e '\@QT_DISABLE_DEPRECATED_BEFORE=@s|0x050F00|0x050000|'
%GIT commit -m "enable some deprecated API" -a
%build
%if 0%{?use_gitbare} >= 1
cd %{name}
%endif
export QT_DIR=%{_libdir}/qt5
export LD_LIBRARY_PATH=$(pwd)/%{_vpath_builddir}/dist
%cmake \
-DCMAKE_SKIP_RPATH=TRUE \
%{nil}
%cmake_build
%install
%if 0%{?use_gitbare} >= 1
cd %{name}
%endif
%cmake_install
# Install all files manually...
# 0. Documents
cp -a \
LICENSE.3rd_party.txt \
LICENSE.txt \
..
pushd %_vpath_builddir
# 1-0 bindir
mkdir -p %{buildroot}%{_bindir}
install -cpm 0755 %{SOURCE10} %{buildroot}%{_bindir}/%{name}
# 1-1 libraries
mkdir -p %{buildroot}%{_libdir}/%{name}
cp -a dist/* %{buildroot}%{_libdir}/%{name}/
rm -f %{buildroot}%{_libdir}/%{name}/*.a
# Back to the top directory
popd
# 1-2 data files
mkdir -p %{buildroot}%{_datadir}/%{name}/
cp -a data %{buildroot}%{_datadir}/%{name}
ln -sf ../../../%{_datadir}/%{name}/data %{buildroot}%{_libdir}/%{name}/data
pushd ./etc/shared
# 1-11 hicolor
mkdir -p %{buildroot}%{_datadir}/icons/hicolor/32x32/mimetypes/
cp -p application-x-ugene-ext.png %{buildroot}/%{_datadir}/icons/hicolor/32x32/mimetypes/
# 1-12 mime
mkdir -p %{buildroot}%{_datadir}/mime/packages
cp -p application-x-ugene.xml %{buildroot}/%{_datadir}/mime/packages
# 1-13 man file
mkdir -p %{buildroot}%{_mandir}/man1
cp -p %{name}.1* %{buildroot}/%{_mandir}/man1
# 1-14 desktop files
mkdir -p %{buildroot}%{_datadir}/applications/
cp -p %{name}.desktop %{buildroot}/%{_datadir}/applications/
# 1-15 icons
mkdir -p %{buildroot}%{_datadir}/pixmaps
cp -p %{name}.{png,xpm} %{buildroot}%{_datadir}/pixmaps
popd
%check
desktop-file-validate %{buildroot}%{_datadir}/applications/%{name}.desktop
%files
%license LICENSE.txt
%license LICENSE.3rd_party.txt
%{_bindir}/%{name}
%dir %{_libdir}/%{name}/
%{_libdir}/%{name}/lib*.so
%dir %{_libdir}/%{name}/plugins/
%{_libdir}/%{name}/plugins/*.license
%{_libdir}/%{name}/plugins/*.plugin
%{_libdir}/%{name}/plugins/lib*.so
%{_libdir}/%{name}/transl_*.qm
%{_libdir}/%{name}/%{name}
%{_libdir}/%{name}/%{name}cl
%{_libdir}/%{name}/%{name}m
%{_libdir}/%{name}/%{name}ui
%{_libdir}/%{name}/plugins_checker
%dir %{_datadir}/%{name}/
%{_datadir}/%{name}/data/
%{_libdir}/%{name}/data
%{_datadir}/applications/%{name}.desktop
%{_datadir}/pixmaps/ugene.*
%{_datadir}/icons/hicolor/32x32/mimetypes/application-x-ugene-ext.png
%{_datadir}/mime/packages/*.xml
%{_mandir}/man1/%{name}.1*
%changelog
* Sun Nov 30 2025 Mamoru TASAKA <mtasaka@fedoraproject.org> - 53.0-1
- 53.0
* Fri Jul 25 2025 Fedora Release Engineering <releng@fedoraproject.org> - 52.1-3
- Rebuilt for https://fedoraproject.org/wiki/Fedora_43_Mass_Rebuild
* Fri Jul 18 2025 Mamoru TASAKA <mtasaka@fedoraproject.org> - 52.1-2
- Fix data files symlink
* Thu May 08 2025 Mamoru TASAKA <mtasaka@fedoraproject.org> - 52.1-1
- 52.1
* Fri Jan 24 2025 Mamoru TASAKA <mtasaka@fedoraproject.org> - 52.0-1
- 52.0
* Fri Jan 17 2025 Mamoru TASAKA <mtasaka@fedoraproject.org> - 51.0-2
- Support C23 strict function prototype
* Thu Sep 26 2024 Mamoru TASAKA <mtasaka@fedoraproject.org> - 51.0-1
- 51.0
* Wed Aug 7 2024 Miroslav Suchý <msuchy@redhat.com> - 50.0-3
- convert license to SPDX
* Sat Jul 20 2024 Fedora Release Engineering <releng@fedoraproject.org> - 50.0-2
- Rebuilt for https://fedoraproject.org/wiki/Fedora_41_Mass_Rebuild
* Sun Apr 14 2024 Mamoru TASAKA <mtasaka@fedoraproject.org> - 50.0-1
- 50.0
* Sat Jan 27 2024 Fedora Release Engineering <releng@fedoraproject.org> - 49.1-3
- Rebuilt for https://fedoraproject.org/wiki/Fedora_40_Mass_Rebuild
* Mon Jan 22 2024 Mamoru TASAKA <mtasaka@fedoraproject.org> - 49.1-2
- Fix -Wnarrowing on non x86(-64) arch detected by gcc14
* Tue Nov 28 2023 Mamoru TASAKA <mtasaka@fedoraproject.org> - 49.1-1
- 49.1
* Thu Nov 9 2023 Mamoru TASAKA <mtasaka@fedoraproject.org> - 49.0-1
- 49.0
* Tue Sep 5 2023 Mamoru TASAKA <mtasaka@fedoraproject.org> - 48.1-1
- 48.1
* Thu Aug 10 2023 Mamoru TASAKA <mtasaka@fedoraproject.org> - 48.0-1
- 48.0
* Sat Jul 22 2023 Mamoru TASAKA <mtasaka@fedoraproject.org> - 47.0-2
- Rebuilt for https://fedoraproject.org/wiki/Fedora_39_Mass_Rebuild
* Tue May 23 2023 Mamoru TASAKA <mtasaka@fedoraproject.org> - 47.0-1
- 47.0
* Fri Feb 24 2023 Mamoru TASAKA <mtasaka@fedoraproject.org> - 46.0-1
- 46.0
* Sat Jan 21 2023 Fedora Release Engineering <releng@fedoraproject.org> - 45.1-2.1
- Rebuilt for https://fedoraproject.org/wiki/Fedora_38_Mass_Rebuild
* Wed Jan 18 2023 Mamoru TASAKA <mtasaka@fedoraproject.org> - 45.1-2
- Header file inclusion fix for gcc13
* Sun Jan 1 2023 Mamoru TASAKA <mtasaka@fedoraproject.org> - 45.1-1
- A Happy New Year 45.1 release
* Tue Dec 20 2022 Florian Weimer <fweimer@redhat.com> - 45.0-2
- Apply upstream patch to fix C99 compatibility issue
* Sun Nov 20 2022 Mamoru TASAKA <mtasaka@fedoraproject.org> - 45.0-1
- 45.0
* Sun Aug 21 2022 Mamoru TASAKA <mtasaka@fedoraproject.org> - 44.0-1
- 44.0
* Sat Jul 23 2022 Fedora Release Engineering <releng@fedoraproject.org> - 43.0-2.1
- Rebuilt for https://fedoraproject.org/wiki/Fedora_37_Mass_Rebuild
* Mon Jun 6 2022 Mamoru TASAKA <mtasaka@fedoraproject.org> - 43.0-1
- 43.0
* Wed Mar 9 2022 Mamoru TASAKA <mtasaka@fedoraproject.org> - 42.0-1
- 42.0
* Sat Jan 22 2022 Fedora Release Engineering <releng@fedoraproject.org> - 41.0-1.1
- Rebuilt for https://fedoraproject.org/wiki/Fedora_36_Mass_Rebuild
* Sat Dec 4 2021 Mamoru TASAKA <mtasaka@fedoraproject.org> - 41.0-1
- 41.0
* Wed Nov 17 2021 Mamoru TASAKA <mtasaka@fedoraproject.org> - 40.1-2
- Surely remove nonfree code from tarball
* Tue Nov 9 2021 Mamoru TASAKA <mtasaka@fedoraproject.org> - 40.1-1
- 40.1
* Fri Jul 23 2021 Fedora Release Engineering <releng@fedoraproject.org> - 34.0-7
- Rebuilt for https://fedoraproject.org/wiki/Fedora_35_Mass_Rebuild
* Wed Jan 27 2021 Fedora Release Engineering <releng@fedoraproject.org> - 34.0-6
- Rebuilt for https://fedoraproject.org/wiki/Fedora_34_Mass_Rebuild
* Mon Nov 23 07:55:33 CET 2020 Jan Grulich <jgrulich@redhat.com> - 34.0-5
- rebuild (qt5)
* Sun Oct 18 2020 Jeff Law <law@redhat.com> - 34.0-4
- Fix missing #includes for gcc-11
* Fri Sep 11 2020 Jan Grulich <jgrulich@redhat.com> - 34.0-3
- rebuild (qt5)
* Wed Jul 29 2020 Fedora Release Engineering <releng@fedoraproject.org> - 34.0-2
- Rebuilt for https://fedoraproject.org/wiki/Fedora_33_Mass_Rebuild
* Wed Apr 15 2020 Rex Dieter <rdieter@fedoraproject.org> - 34.0-1
- ugene-34.0
- update Source0 URL
- no longer uses qt5 private api (yay)
- use %%check
* Mon Apr 06 2020 Rex Dieter <rdieter@fedoraproject.org> - 33.0-13
- rebuild (qt5)
* Fri Jan 31 2020 Fedora Release Engineering <releng@fedoraproject.org> - 33.0-12
- Rebuilt for https://fedoraproject.org/wiki/Fedora_32_Mass_Rebuild
* Mon Dec 09 2019 Jan Grulich <jgrulich@redhat.com> - 33.0-11
- rebuild (qt5)
* Sat Oct 05 2019 Yuliya Algaer <yalgaer@redhat.com> - 33.0-10
- New release
* Wed Sep 25 2019 Jan Grulich <jgrulich@redhat.com> - 1.31.1-7
- rebuild (qt5)
- workaround FTBFS using -fpermissive (#1736931)
* Sat Jul 27 2019 Fedora Release Engineering <releng@fedoraproject.org> - 1.31.1-6
- Rebuilt for https://fedoraproject.org/wiki/Fedora_31_Mass_Rebuild
* Mon Jun 17 2019 Jan Grulich <jgrulich@redhat.com> - 1.31.1-5
- rebuild (qt5)
* Sun Mar 03 2019 Rex Dieter <rdieter@fedoraproject.org> - 1.31.1-4
- rebuild (qt5)
* Sun Feb 03 2019 Fedora Release Engineering <releng@fedoraproject.org> - 1.31.1-3
- Rebuilt for https://fedoraproject.org/wiki/Fedora_30_Mass_Rebuild
* Thu Dec 13 2018 Rex Dieter <rdieter@fedoraproject.org> - 1.31.1-2
- rebuild (qt5)
* Thu Oct 25 2018 Yuliya Algaer <yalgaer@fedoraproject.com> - 1.31.1-1
- New upstream release
* Fri Aug 24 2018 Yuliya Algaer <yalgaer@fedoraproject.org> - 1.31.0-6
- New upstream release
* Sat Jul 14 2018 Fedora Release Engineering <releng@fedoraproject.org> - 1.30.0-25
- Rebuilt for https://fedoraproject.org/wiki/Fedora_29_Mass_Rebuild
* Thu Jun 21 2018 Rex Dieter <rdieter@fedoraproject.org> - 1.30.0-24
- rebuild (qt5)
* Mon Jun 11 2018 Yuliya Algaer <yalgaer@fedoraproject.org> - 1.30.0-23
- New upstream release
* Sun May 27 2018 Rex Dieter <rdieter@fedoraproject.org> - 1.29.0-7
- rebuild (qt5)
* Wed Feb 14 2018 Jan Grulich <jgrulich@redhat.com> - 1.29.0-6
- rebuild (qt5)
* Fri Feb 09 2018 Fedora Release Engineering <releng@fedoraproject.org> - 1.29.0-5
- Rebuilt for https://fedoraproject.org/wiki/Fedora_28_Mass_Rebuild
* Thu Jan 18 2018 Igor Gnatenko <ignatenkobrain@fedoraproject.org> - 1.29.0-4
- Remove obsolete scriptlets
* Tue Jan 02 2018 Kevin Kofler <Kevin@tigcc.ticalc.org> - 1.29.0-3
- Fix FTBFS with Qt 5.10
* Mon Jan 01 2018 Rex Dieter <rdieter@fedoraproject.org> - 1.29.0-2
- rebuild (qt5)
* Sun Dec 31 2017 Yuliya Algaer <yalgaer@fedoraproject.org> - 1.29.0-1
- New upstream release.
* Wed Dec 20 2017 Jan Grulich <jgrulich@redhat.com> - 1.28.1-3
- rebuild (qt5)
* Mon Nov 27 2017 Rex Dieter <rdieter@fedoraproject.org> - 1.28.1-2
- rebuild (qt5)
* Tue Nov 21 2017 Yuliya Algaer <yalgaer@fedoraproject.org> - 1.28.1-1
- New upstream release.
* Tue Oct 10 2017 Rex Dieter <rdieter@fedoraproject.org> - 1.27.0-8
- rebuild (qt5)
* Mon Aug 28 2017 Yuliya Algaer <yalgaer@fedoraproject.org> - 1.27.0-7
- New upstream release
* Thu Aug 03 2017 Fedora Release Engineering <releng@fedoraproject.org> - 1.26.3-4
- Rebuilt for https://fedoraproject.org/wiki/Fedora_27_Binutils_Mass_Rebuild
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