From 6a7a6f7c2f87a274696dd25effaea02e21da50f3 Mon Sep 17 00:00:00 2001 From: Yuliya Algaer Date: Fri, 30 Jun 2017 01:03:48 +0700 Subject: [PATCH 1/5] Update to 1.26.3 --- sources | 2 +- ugene.spec | 5 ++++- 2 files changed, 5 insertions(+), 2 deletions(-) diff --git a/sources b/sources index c3b0bf9..3f8c102 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-1.26.1.tar.gz) = 5653ef0e5b054a3a8b044c323581861c4ab5f83686b8f8bc810e96eb4771b24160566ff4bf4346984a1fe324ad9a34465ee8610e4ec4b5fa0e01b536dd0c21e3 +SHA512 (ugene-1.26.3.tar.gz) = 6f73d94b81a1b8513e1be96231499fe58cb8a00f0dc4a701d0ad8a467f29a3425ad6980459a5199dd6e83a1886f84a8e3cc8586946d53f18a3f90de06c7b25e4 diff --git a/ugene.spec b/ugene.spec index a779989..7c29b59 100644 --- a/ugene.spec +++ b/ugene.spec @@ -1,6 +1,6 @@ Name: ugene Summary: Integrated bioinformatics toolkit -Version: 1.26.1 +Version: 1.26.3 Release: 1%{?dist} #The entire source code is GPLv2+ except: #file src/libs_3rdparty/qtbindings_core/src/qtscriptconcurrent.h which is GPLv2 @@ -107,6 +107,9 @@ fi %{_mandir}/man1/* %changelog +* Fri Jun 30 2017 Yuliya Algaer - 1.26.3-1 +- New minor release. + * Mon Feb 27 2017 Yuliya Algaer - 1.26.1-1 - Minor fix. From 3ed3494747404592031cdb91ba75f67f83992737 Mon Sep 17 00:00:00 2001 From: Yuliya Algaer Date: Mon, 28 Aug 2017 13:49:02 +0700 Subject: [PATCH 2/5] Update to 1.27.0 --- sources | 2 +- ugene-1.22.0-dont_hardcode_includes.patch | 24 ------------- ugene-1.22.0-mime_path.patch | 24 ------------- ugene.spec | 44 +++-------------------- 4 files changed, 6 insertions(+), 88 deletions(-) delete mode 100644 ugene-1.22.0-dont_hardcode_includes.patch delete mode 100644 ugene-1.22.0-mime_path.patch diff --git a/sources b/sources index 3f8c102..056c83a 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-1.26.3.tar.gz) = 6f73d94b81a1b8513e1be96231499fe58cb8a00f0dc4a701d0ad8a467f29a3425ad6980459a5199dd6e83a1886f84a8e3cc8586946d53f18a3f90de06c7b25e4 +SHA512 (ugene-1.27.0.tar.gz) = 75905c546ed2aa10c5595a90406b2f00d717641573961fff07df4b8c46cf807d6995537560f9178cc84b8b80fd8bd031a1f59904557d1f8f9ba8ad916156b071 diff --git a/ugene-1.22.0-dont_hardcode_includes.patch b/ugene-1.22.0-dont_hardcode_includes.patch deleted file mode 100644 index 6bc26e1..0000000 --- a/ugene-1.22.0-dont_hardcode_includes.patch +++ /dev/null @@ -1,24 +0,0 @@ -diff -up ugene-1.22.0/src/libs_3rdparty/samtools/samtools.pri.dont_hardcode_includes ugene-1.22.0/src/libs_3rdparty/samtools/samtools.pri ---- ugene-1.22.0/src/libs_3rdparty/samtools/samtools.pri.dont_hardcode_includes 2016-03-31 07:21:56.000000000 -0500 -+++ ugene-1.22.0/src/libs_3rdparty/samtools/samtools.pri 2016-06-02 17:49:02.383069490 -0500 -@@ -3,7 +3,7 @@ UGENE_RELATIVE_DESTDIR = '' - - TEMPLATE = lib - CONFIG +=thread debug_and_release staticlib warn_off --INCLUDEPATH += src src/samtools ../../include /usr/include -+INCLUDEPATH += src src/samtools ../../include - win32 : INCLUDEPATH += src/samtools/win32 - DEFINES+="_FILE_OFFSET_BITS=64" _LARGEFILE64_SOURCE _USE_KNETFILE - win32 : DEFINES += _USE_MATH_DEFINES "inline=__inline" "__func__=__FUNCTION__" "R_OK=4" "atoll=_atoi64" "alloca=_alloca" -diff -up ugene-1.22.0/src/plugins_3rdparty/variants/variants.pri.dont_hardcode_includes ugene-1.22.0/src/plugins_3rdparty/variants/variants.pri ---- ugene-1.22.0/src/plugins_3rdparty/variants/variants.pri.dont_hardcode_includes 2016-03-31 07:22:09.000000000 -0500 -+++ ugene-1.22.0/src/plugins_3rdparty/variants/variants.pri 2016-06-02 20:26:35.265356432 -0500 -@@ -20,7 +20,7 @@ use_bundled_zlib() { - win32 : LIBS += -lwsock32 - - --INCLUDEPATH += src ../../include /usr/include -+INCLUDEPATH += src ../../include - INCLUDEPATH += ../../libs_3rdparty/samtools/src/samtools - INCLUDEPATH += ../../libs_3rdparty/samtools/src - INCLUDEPATH += ../../libs_3rdparty/samtools/src/samtools/bcftools diff --git a/ugene-1.22.0-mime_path.patch b/ugene-1.22.0-mime_path.patch deleted file mode 100644 index 7ad7556..0000000 --- a/ugene-1.22.0-mime_path.patch +++ /dev/null @@ -1,24 +0,0 @@ -diff -up ugene-1.22.0/src/ugene_globals.pri.mime_path ugene-1.22.0/src/ugene_globals.pri ---- ugene-1.22.0/src/ugene_globals.pri.mime_path 2016-06-02 20:26:59.803440631 -0500 -+++ ugene-1.22.0/src/ugene_globals.pri 2016-06-03 05:39:34.696544247 -0500 -@@ -47,7 +47,7 @@ isEmpty( UGENE_INSTALL_DESKTOP ) : UGENE - isEmpty( UGENE_INSTALL_PIXMAPS ) : UGENE_INSTALL_PIXMAPS = $$INSTALL_DATADIR/pixmaps - isEmpty( UGENE_INSTALL_DATA ) : UGENE_INSTALL_DATA = $$INSTALL_DATADIR/ugene/data - isEmpty( UGENE_INSTALL_ICONS ) : UGENE_INSTALL_ICONS = $$INSTALL_DATADIR/icons --isEmpty( UGENE_INSTALL_MIME ) : UGENE_INSTALL_MIME = $$INSTALL_DATADIR/mime -+isEmpty( UGENE_INSTALL_MIME ) : UGENE_INSTALL_MIME = $$INSTALL_DATADIR/mime/packages - isEmpty( UGENE_INSTALL_DIR ) : UGENE_INSTALL_DIR = $$INSTALL_LIBDIR/ugene - isEmpty( UGENE_INSTALL_BINDIR ) : UGENE_INSTALL_BINDIR = $$INSTALL_BINDIR - isEmpty( UGENE_INSTALL_MAN ) : UGENE_INSTALL_MAN = $$INSTALL_MANDIR/man1 -diff -up ugene-1.22.0/ugene.pro.mime_path ugene-1.22.0/ugene.pro ---- ugene-1.22.0/ugene.pro.mime_path 2016-03-31 07:21:56.000000000 -0500 -+++ ugene-1.22.0/ugene.pro 2016-06-03 05:46:09.723758610 -0500 -@@ -218,7 +218,7 @@ unix { - mime.path = $$UGENE_INSTALL_MIME - - icons.files += installer/_common_data/application-x-ugene-ext.png -- icons.path = $$UGENE_INSTALL_ICONS -+ icons.path = $$UGENE_INSTALL_ICONS/hicolor/32x32/mimetypes/ - - - INSTALLS += binscript ugene_starter transl plugins scripts data desktop pixmaps mime icons manual diff --git a/ugene.spec b/ugene.spec index f68d6fd..a07c849 100644 --- a/ugene.spec +++ b/ugene.spec @@ -1,7 +1,7 @@ Name: ugene Summary: Integrated bioinformatics toolkit -Version: 1.26.3 -Release: 4%{?dist} +Version: 1.27.0 +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 @@ -10,15 +10,6 @@ Group: Applications/Engineering URL: http://ugene.unipro.ru Source0: http://ugene.unipro.ru/downloads/%{name}-%{version}.tar.gz -# upstreamable , don't hard-code include paths /usr/include in particular -Patch1: ugene-1.22.0-dont_hardcode_includes.patch -# upstreamable, install mime definitions to prefix/mime/packages, and icon -# to hicolor themed dir per xdg specs -# TODO/FIXME: ugene.desktop Exec= key should be amended per -# https://specifications.freedesktop.org/desktop-entry-spec/latest/ar01s06.html -# depending if ugene supports remote/local files and single/multiple files at once -Patch2: ugene-1.22.0-mime_path.patch - BuildRequires: desktop-file-utils BuildRequires: mesa-libGLU-devel BuildRequires: procps-devel @@ -53,9 +44,6 @@ is a designer for custom bioinformatics workflows. %prep %setup -q -%patch1 -p1 -b .dont_hardcode_includes -%patch2 -p1 -b .mime_paths - %build %{qmake_qt5} -r \ INSTALL_BINDIR=%{_bindir} \ @@ -107,30 +95,8 @@ fi %{_mandir}/man1/* %changelog +* Mon Aug 28 2017 Yuliya Algaer - 1.27.0-1 +- New upstream release + * Thu Aug 03 2017 Fedora Release Engineering - 1.26.3-4 - Rebuilt for https://fedoraproject.org/wiki/Fedora_27_Binutils_Mass_Rebuild - -* Thu Jul 27 2017 Fedora Release Engineering - 1.26.3-3 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_27_Mass_Rebuild - -* Wed Jul 19 2017 Rex Dieter - 1.26.3-2 -- rebuild (qt5) - -* Thu Jun 29 2017 Yuliya Algaer - 1.26.3-1 -- New minor release. - -* Sun May 14 2017 Rex Dieter - 1.26.1-3 -- rebuild (qt5) - -* Fri Mar 31 2017 Rex Dieter - 1.26.1-2 -- rebuild (qt5) - -* Mon Feb 27 2017 Yuliya Algaer - 1.26.1-1 -- Minor fix. - -* Mon Feb 13 2017 Yuliya Algaer - 1.26.0-2 -- Minor fix. - -* Fri Feb 10 2017 Yuliya Algaer - 1.26.0-1 -- New upstream version - From ba77ce8d81322f7dce8a11254d77fe4c1c737879 Mon Sep 17 00:00:00 2001 From: Yuliya Algaer Date: Mon, 28 Aug 2017 15:38:10 +0700 Subject: [PATCH 3/5] Update to 1.27.0 --- sources | 2 +- ugene-1.22.0-dont_hardcode_includes.patch | 24 ------------------- ugene-1.22.0-mime_path.patch | 24 ------------------- ugene.spec | 29 ++++------------------- 4 files changed, 6 insertions(+), 73 deletions(-) delete mode 100644 ugene-1.22.0-dont_hardcode_includes.patch delete mode 100644 ugene-1.22.0-mime_path.patch diff --git a/sources b/sources index 3f8c102..056c83a 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-1.26.3.tar.gz) = 6f73d94b81a1b8513e1be96231499fe58cb8a00f0dc4a701d0ad8a467f29a3425ad6980459a5199dd6e83a1886f84a8e3cc8586946d53f18a3f90de06c7b25e4 +SHA512 (ugene-1.27.0.tar.gz) = 75905c546ed2aa10c5595a90406b2f00d717641573961fff07df4b8c46cf807d6995537560f9178cc84b8b80fd8bd031a1f59904557d1f8f9ba8ad916156b071 diff --git a/ugene-1.22.0-dont_hardcode_includes.patch b/ugene-1.22.0-dont_hardcode_includes.patch deleted file mode 100644 index 6bc26e1..0000000 --- a/ugene-1.22.0-dont_hardcode_includes.patch +++ /dev/null @@ -1,24 +0,0 @@ -diff -up ugene-1.22.0/src/libs_3rdparty/samtools/samtools.pri.dont_hardcode_includes ugene-1.22.0/src/libs_3rdparty/samtools/samtools.pri ---- ugene-1.22.0/src/libs_3rdparty/samtools/samtools.pri.dont_hardcode_includes 2016-03-31 07:21:56.000000000 -0500 -+++ ugene-1.22.0/src/libs_3rdparty/samtools/samtools.pri 2016-06-02 17:49:02.383069490 -0500 -@@ -3,7 +3,7 @@ UGENE_RELATIVE_DESTDIR = '' - - TEMPLATE = lib - CONFIG +=thread debug_and_release staticlib warn_off --INCLUDEPATH += src src/samtools ../../include /usr/include -+INCLUDEPATH += src src/samtools ../../include - win32 : INCLUDEPATH += src/samtools/win32 - DEFINES+="_FILE_OFFSET_BITS=64" _LARGEFILE64_SOURCE _USE_KNETFILE - win32 : DEFINES += _USE_MATH_DEFINES "inline=__inline" "__func__=__FUNCTION__" "R_OK=4" "atoll=_atoi64" "alloca=_alloca" -diff -up ugene-1.22.0/src/plugins_3rdparty/variants/variants.pri.dont_hardcode_includes ugene-1.22.0/src/plugins_3rdparty/variants/variants.pri ---- ugene-1.22.0/src/plugins_3rdparty/variants/variants.pri.dont_hardcode_includes 2016-03-31 07:22:09.000000000 -0500 -+++ ugene-1.22.0/src/plugins_3rdparty/variants/variants.pri 2016-06-02 20:26:35.265356432 -0500 -@@ -20,7 +20,7 @@ use_bundled_zlib() { - win32 : LIBS += -lwsock32 - - --INCLUDEPATH += src ../../include /usr/include -+INCLUDEPATH += src ../../include - INCLUDEPATH += ../../libs_3rdparty/samtools/src/samtools - INCLUDEPATH += ../../libs_3rdparty/samtools/src - INCLUDEPATH += ../../libs_3rdparty/samtools/src/samtools/bcftools diff --git a/ugene-1.22.0-mime_path.patch b/ugene-1.22.0-mime_path.patch deleted file mode 100644 index 7ad7556..0000000 --- a/ugene-1.22.0-mime_path.patch +++ /dev/null @@ -1,24 +0,0 @@ -diff -up ugene-1.22.0/src/ugene_globals.pri.mime_path ugene-1.22.0/src/ugene_globals.pri ---- ugene-1.22.0/src/ugene_globals.pri.mime_path 2016-06-02 20:26:59.803440631 -0500 -+++ ugene-1.22.0/src/ugene_globals.pri 2016-06-03 05:39:34.696544247 -0500 -@@ -47,7 +47,7 @@ isEmpty( UGENE_INSTALL_DESKTOP ) : UGENE - isEmpty( UGENE_INSTALL_PIXMAPS ) : UGENE_INSTALL_PIXMAPS = $$INSTALL_DATADIR/pixmaps - isEmpty( UGENE_INSTALL_DATA ) : UGENE_INSTALL_DATA = $$INSTALL_DATADIR/ugene/data - isEmpty( UGENE_INSTALL_ICONS ) : UGENE_INSTALL_ICONS = $$INSTALL_DATADIR/icons --isEmpty( UGENE_INSTALL_MIME ) : UGENE_INSTALL_MIME = $$INSTALL_DATADIR/mime -+isEmpty( UGENE_INSTALL_MIME ) : UGENE_INSTALL_MIME = $$INSTALL_DATADIR/mime/packages - isEmpty( UGENE_INSTALL_DIR ) : UGENE_INSTALL_DIR = $$INSTALL_LIBDIR/ugene - isEmpty( UGENE_INSTALL_BINDIR ) : UGENE_INSTALL_BINDIR = $$INSTALL_BINDIR - isEmpty( UGENE_INSTALL_MAN ) : UGENE_INSTALL_MAN = $$INSTALL_MANDIR/man1 -diff -up ugene-1.22.0/ugene.pro.mime_path ugene-1.22.0/ugene.pro ---- ugene-1.22.0/ugene.pro.mime_path 2016-03-31 07:21:56.000000000 -0500 -+++ ugene-1.22.0/ugene.pro 2016-06-03 05:46:09.723758610 -0500 -@@ -218,7 +218,7 @@ unix { - mime.path = $$UGENE_INSTALL_MIME - - icons.files += installer/_common_data/application-x-ugene-ext.png -- icons.path = $$UGENE_INSTALL_ICONS -+ icons.path = $$UGENE_INSTALL_ICONS/hicolor/32x32/mimetypes/ - - - INSTALLS += binscript ugene_starter transl plugins scripts data desktop pixmaps mime icons manual diff --git a/ugene.spec b/ugene.spec index 7c29b59..a07c849 100644 --- a/ugene.spec +++ b/ugene.spec @@ -1,6 +1,6 @@ Name: ugene Summary: Integrated bioinformatics toolkit -Version: 1.26.3 +Version: 1.27.0 Release: 1%{?dist} #The entire source code is GPLv2+ except: #file src/libs_3rdparty/qtbindings_core/src/qtscriptconcurrent.h which is GPLv2 @@ -10,15 +10,6 @@ Group: Applications/Engineering URL: http://ugene.unipro.ru Source0: http://ugene.unipro.ru/downloads/%{name}-%{version}.tar.gz -# upstreamable , don't hard-code include paths /usr/include in particular -Patch1: ugene-1.22.0-dont_hardcode_includes.patch -# upstreamable, install mime definitions to prefix/mime/packages, and icon -# to hicolor themed dir per xdg specs -# TODO/FIXME: ugene.desktop Exec= key should be amended per -# https://specifications.freedesktop.org/desktop-entry-spec/latest/ar01s06.html -# depending if ugene supports remote/local files and single/multiple files at once -Patch2: ugene-1.22.0-mime_path.patch - BuildRequires: desktop-file-utils BuildRequires: mesa-libGLU-devel BuildRequires: procps-devel @@ -53,9 +44,6 @@ is a designer for custom bioinformatics workflows. %prep %setup -q -%patch1 -p1 -b .dont_hardcode_includes -%patch2 -p1 -b .mime_paths - %build %{qmake_qt5} -r \ INSTALL_BINDIR=%{_bindir} \ @@ -107,15 +95,8 @@ fi %{_mandir}/man1/* %changelog -* Fri Jun 30 2017 Yuliya Algaer - 1.26.3-1 -- New minor release. - -* Mon Feb 27 2017 Yuliya Algaer - 1.26.1-1 -- Minor fix. - -* Mon Feb 13 2017 Yuliya Algaer - 1.26.0-2 -- Minor fix. - -* Fri Feb 10 2017 Yuliya Algaer - 1.26.0-1 -- New upstream version +* Mon Aug 28 2017 Yuliya Algaer - 1.27.0-1 +- New upstream release +* Thu Aug 03 2017 Fedora Release Engineering - 1.26.3-4 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_27_Binutils_Mass_Rebuild From 18ddfcb653ba0aea9c8e5e3836d6b189cb5b2000 Mon Sep 17 00:00:00 2001 From: Yuliya Algaer Date: Tue, 21 Nov 2017 10:49:49 +0700 Subject: [PATCH 4/5] Update to 1.28.1 --- sources | 2 +- ugene.spec | 7 +++++-- 2 files changed, 6 insertions(+), 3 deletions(-) diff --git a/sources b/sources index 056c83a..fc93d22 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-1.27.0.tar.gz) = 75905c546ed2aa10c5595a90406b2f00d717641573961fff07df4b8c46cf807d6995537560f9178cc84b8b80fd8bd031a1f59904557d1f8f9ba8ad916156b071 +SHA512 (ugene-1.28.1.tar.gz) = 0e6678febd0420eb67be39042ebc443594cbf08e8cbe2a22a1786fedae120c65e2cabdf5d19b51d2f0ff83c2bcfa06000b16821ee79a6a99831c46a71d2570a7 diff --git a/ugene.spec b/ugene.spec index 965c9f2..5d31b46 100644 --- a/ugene.spec +++ b/ugene.spec @@ -1,7 +1,7 @@ Name: ugene Summary: Integrated bioinformatics toolkit -Version: 1.27.0 -Release: 8%{?dist} +Version: 1.28.1 +Release: 1%{?dist} #The entire source code is GPLv2+ except: #file src/libs_3rdparty/qtbindings_core/src/qtscriptconcurrent.h which is GPLv2 @@ -96,6 +96,9 @@ fi %{_mandir}/man1/* %changelog +* Tue Nov 21 2017 Yuliya Algaer - 1.28.1-1 +- New upstream release + * Tue Oct 10 2017 Rex Dieter - 1.27.0-8 - rebuild (qt5) From 5a5e33b43fdd84e33e8cab783c94d4f3f3a6b21e Mon Sep 17 00:00:00 2001 From: Rex Dieter Date: Mon, 29 Jan 2018 06:16:32 -0600 Subject: [PATCH 5/5] rebuild (qt5) --- ugene.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/ugene.spec b/ugene.spec index 5d31b46..ef9cbce 100644 --- a/ugene.spec +++ b/ugene.spec @@ -1,7 +1,7 @@ Name: ugene Summary: Integrated bioinformatics toolkit Version: 1.28.1 -Release: 1%{?dist} +Release: 2%{?dist} #The entire source code is GPLv2+ except: #file src/libs_3rdparty/qtbindings_core/src/qtscriptconcurrent.h which is GPLv2 @@ -96,6 +96,9 @@ fi %{_mandir}/man1/* %changelog +* Mon Jan 29 2018 Rex Dieter - 1.28.1-2 +- rebuild (qt5) + * Tue Nov 21 2017 Yuliya Algaer - 1.28.1-1 - New upstream release