%global   use_release_branch  0

%if 0%{?use_release_branch} < 1

# master

%global	gitdate		20230116

%global	gitcommit		959b7d5775242c84cbec866897676f366fe372b1

# New git commit with non-free part removed using "git filter-branch"

%global	gitcommit_free		ce0246a7c9d15dd96fb81c67b514485cf9e2b844

%else

# currently 41.0 branch

%global	gitdate		20211117

%global	gitcommit		2d776cc668bc5019452e25ecc330c88093e75c48

# New git commit with non-free part using "git filter-branch"

%global	gitcommit_free		f995e33068c5959c1bab249cd04ed3776e9b2d96

%endif

%global	shortcommit	%(c=%{gitcommit}; echo ${c:0:7})

%global	git_version	D%{gitdate}git%{shortcommit}

%global	tarballdate	20230117

%global	tarballtime	1409

%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	mainrel		2.1

%undefine	prever

%if		0%{?use_release} >= 1

%global	fedorarel		%{?prever:0.}%{mainrel}%{?prever:.%{prerpmver}}

%endif

%if		0%{?use_gitbare} >= 1

%global	fedorarel		%{mainrel}.%{git_version}

%endif

Name:		ugene

Summary:	Integrated bioinformatics toolkit

Version:	45.1

Release:	%{fedorarel}%{?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

License:	GPLv2+ and GPLv2

URL:		http://ugene.net

%if	0%{?use_release} >= 1

#Source0:	https://github.com/ugeneunipro/ugene/archive/%{version}.tar.gz/#/%{name}-%{version}.tar.gz

# Removing non-free part

Source0:	%{name}-free-%{version}.tar.gz

# Source0 is created by # env VERSION=%%{version} 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-45.1-gcc13-header-inclusion.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-42.0-plugins_3rdparty-hmm2-nosse-arch.patch

Patch105:	ugene-40.1-libs_3rdparty-breakpad-arch-port.patch

Patch106:	ugene-43.0-git-plgins-smith_waterman-nonsse2-arch.patch

Patch107:	ugene-40.1-qbswap-bigendian-workaround.patch

Patch108:	ugene-43.x-wrong-elif-SendReportDialog.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(Qt5Network)

BuildRequires:	cmake(Qt5PrintSupport)

BuildRequires:	cmake(Qt5Script)

BuildRequires:	cmake(Qt5ScriptTools)

BuildRequires:	cmake(Qt5Sql)

BuildRequires:	cmake(Qt5Svg)

BuildRequires:	cmake(Qt5Test)

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

# Umm...

sed -i.desktop ugene.pri -e '\@desktop@s|etc/share/|etc/shared/|'

%endif

%if		0%{?use_gitbare} >= 1

%setup -q -c -T -a 0

git clone ./%{name}.git/

cd %{name}

cp -a [A-Z]* ..

git checkout -b %{version}-fedora %{gitcommit_free}

git config user.name "%{name} Fedora maintainer"

git config user.email "%{name}-maintainers@fedoraproject.org"

%endif

%patch1 -p1 -b .gcc13 -Z

	%GIT commit -m "add missing header file" -a

%patch102 -p1 -b .sys_mmap -Z

	%GIT commit -m "libs_3rdparty/breakpad: use C function instead of directly using syscall assemble code" -a

%patch103 -p1 -b .unwind -Z

	%GIT commit -m "libs_3rdparty/breakpad: workaround for arch not supporting unwind" -a

%patch104 -p1 -b .sse -Z

	%GIT commit -m "plugins_3rdparty/hmm2: support architecture not supporting SSE2" -a

%patch105 -p1 -b .port -Z

	%GIT commit -m "libs_3rdparty/breakpad: workaround for arch not ported by the upstream" -a

%patch106 -p1 -b .sse_2 -Z

	%GIT	commit -m "plugins/smith_waterman: support architecture not supporting SSE2" -a

%patch107 -p1 -b .char_bigen -Z

	%GIT	commit -m "src/corelibs/U2Core et al.: Workaround for Qt qbswap issue on Q_BIG_ENDIAN" -a

%patch108 -p1 -b .elif -Z

	%GIT commit -m "ugenem/src/SendReportDialog.cpp: fix wrong elif usage" -a

sed -i.nonfree CMakeLists.txt -e '\@add_subdirectory.*plugins_3rdparty/psipred@d'

sed -i.nonfree ugene.pro -e '\@plugins_3rdparty/psipred@d'

	%GIT commit -m "remove nonfree code" -a

%build

%if		0%{?use_gitbare} >= 1

cd %{name}

%endif

%{qmake_qt5} -r \

	PREFIX=%{_libdir}/%{name} \

	UGENE_EXCLUDE_LIST_ENABLED=1 \

	UGENE_USE_SYSTEM_SQLITE=1 \

	UGENE_USE_BUNDLED_ZLIB=0 \

	UGENE_WITHOUT_NON_FREE=1 \

	%{nil}

%make_build -k

%install

LIBAPPDIR=%{_libdir}/%{name}

%if		0%{?use_gitbare} >= 1

cd %{name}

%endif

make install \

	INSTALL_ROOT=%{buildroot} \

	INSTALL="install -p" \

	%{nil}

# Some needed files are not installed.....

mkdir -p %{buildroot}$LIBAPPDIR

cp -a src/_release/* %{buildroot}$LIBAPPDIR

rm -f %{buildroot}$LIBAPPDIR/*.a

# 1. manually move files...

pushd %{buildroot}

rm -f ./$LIBAPPDIR/LICENSE*

# 1-0 bindir

mkdir -p ./%{_bindir}

install -cpm 0755 %{SOURCE10} ./%{_bindir}/%{name}

# 1-1 data files

mkdir -p ./%{_datadir}/%{name}/

mv ./$LIBAPPDIR/data ./%{_datadir}/%{name}

ln -sf ../../../%{_datadir}/%{name} ./$LIBAPPDIR/data

# 1-11 hicolor

mkdir -p ./%{_datadir}/icons/hicolor/32x32/mimetypes/

mv ./$LIBAPPDIR/application-x-ugene-ext.png ./%{_datadir}/icons/hicolor/32x32/mimetypes/

# 1-12 mime

mkdir -p ./%{_datadir}/mime/packages

mv ./$LIBAPPDIR/application-x-ugene.xml ./%{_datadir}/mime/packages

# 1-13 man file

mkdir -p ./%{_mandir}/man1

mv ./$LIBAPPDIR/%{name}.1* ./%{_mandir}/man1

# 1-14 desktop files

mkdir -p ./%{_datadir}/applications/

mv ./$LIBAPPDIR/%{name}.desktop ./%{_datadir}/applications/

# 1-15 icons

mkdir -p ./%{_datadir}/pixmaps

mv ./$LIBAPPDIR/%{name}.{png,xpm} ./%{_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}/%{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

* 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