[med-svn] [Git][med-team/ugene][master] 4 commits: Install icon
Andreas Tille
gitlab at salsa.debian.org
Thu Jan 31 20:40:02 GMT 2019
Andreas Tille pushed to branch master at Debian Med / ugene
Commits:
9c892061 by Andreas Tille at 2019-01-31T18:15:31Z
Install icon
- - - - -
12b89f9d by Andreas Tille at 2019-01-31T20:12:27Z
Drop unused lintian-overrides
- - - - -
3addfa78 by Andreas Tille at 2019-01-31T20:16:46Z
Add exec code for mime in desktop file
- - - - -
2fb0ac5d by Andreas Tille at 2019-01-31T20:25:45Z
Fix PATHes in d/copyright
- - - - -
9 changed files:
- debian/changelog
- debian/copyright
- debian/patches/add_missing_header.patch
- debian/patches/debian_packaged_libs.patch
- debian/patches/do_not_build_phylip.patch
- + debian/patches/fix_desktop_file.patch
- debian/patches/series
- − debian/ugene-data.lintian-overrides
- debian/ugene.install
Changes:
=====================================
debian/changelog
=====================================
@@ -13,6 +13,7 @@ ugene (1.31.1+dfsg-1) UNRELEASED; urgency=medium
* More Files-Excluded
* debhelper 12
* Point Vcs fields to salsa.debian.org
+ * Drop unused lintian-overrides
-- Andreas Tille <tille at debian.org> Sun, 03 Dec 2017 19:10:03 +0100
=====================================
debian/copyright
=====================================
@@ -168,44 +168,6 @@ License: BSD-3-clause
(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-Files: src/plugins_3rdparty/hmm3/src/hmmer3/*
-Copyright: © 2000-2009 Howard Hughes Medical Institute (and others)
-License: GPL-3+
-
-Files: src/plugins_3rdparty/hmm3/src/hmmer3/easel/*
-Copyright: © 2006-2009 Howard Hughes Medical Institute (and others)
-License: JaneliaFarm
- Redistribution and use in source and binary forms, with or without
- modification, are permitted provided that the following conditions are
- met:
- .
- 1. Redistributions of source code must retain the above copyright
- notice, this list of conditions and the following disclaimer.
- .
- 2. Redistributions in binary form must reproduce the above copyright
- notice, this list of conditions and the following disclaimer in
- the documentation and/or other materials provided with the
- distribution.
- .
- 3. Neither the name of the Howard Hughes Medical Institute nor the
- names of its contributors may be used to endorse or promote
- products derived from this software without specific prior written
- permission.
- .
- THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
- "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
- LIMITED TO, ANY IMPLIED WARRANTIES OF MERCHANTABILITY,
- NON-INFRINGEMENT, OR FITNESS FOR A PARTICULAR PURPOSE ARE
- DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
- LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
- CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
- SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
- REASONABLE ROYALTIES; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
- ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR
- TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE
- USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
- DAMAGE.
-
Files: src/plugins/biostruct3d_view/src/gl2ps/*
Copyright: © 1999-2006 Christophe Geuzaine <geuz at geuz.org>
License: GPL-2+
@@ -263,7 +225,7 @@ License: BSD+Khronos
TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
MATERIALS OR THE USE OR OTHER DEALINGS IN THE MATERIALS.
-Files: src/corelibs/U2Private/src/StackWalker.*
+Files: src/corelibs/U2Private/src/crash_handler/StackWalker.*
Copyright: © 2005-2011 Jochen Kalmbach
License: BSD-2-clause
Redistribution and use in source and binary forms, with or without modification,
=====================================
debian/patches/add_missing_header.patch
=====================================
@@ -1,5 +1,5 @@
Author: Andreas Tille <tille at debian.org>
-Last-Update: Sun, 03 Dec 2017 19:10:03 +0100
+Last-Update: Thu, 31 Jan 2019 21:14:50 +0100
Description: Fix build issue by adding missing headers
--- a/src/plugins/external_tool_support/src/trimmomatic/steps/SlidingWindowStep.cpp
=====================================
debian/patches/debian_packaged_libs.patch
=====================================
@@ -1,18 +1,7 @@
Author: Andreas Tille <tille at debian.org>
-Last-Update: Sun, 03 Dec 2017 19:10:03 +0100
+Last-Update: Thu, 31 Jan 2019 21:14:50 +0100
Description: Replace zlib and sqlite3 by Debian packaged libs
---- a/CMakeLists.txt
-+++ b/CMakeLists.txt
-@@ -35,8 +35,6 @@ set(CMAKE_C_FLAGS_DEBUG "${CMAKE_C_FLAGS
- # 3rd party libs
- add_subdirectory(src/libs_3rdparty/breakpad)
- add_subdirectory(src/libs_3rdparty/samtools)
--add_subdirectory(src/libs_3rdparty/sqlite3)
--add_subdirectory(src/libs_3rdparty/zlib)
-
- # Core libs
- add_subdirectory(src/corelibs/U2Core)
--- a/src/libs_3rdparty/samtools/src/samtools/bam.h
+++ b/src/libs_3rdparty/samtools/src/samtools/bam.h
@@ -61,7 +61,7 @@ typedef BGZF *bamFile;
=====================================
debian/patches/do_not_build_phylip.patch
=====================================
@@ -1,5 +1,5 @@
Author: Andreas Tille <tille at debian.org>
-Last-Update: Sun, 03 Dec 2017 19:10:03 +0100
+Last-Update: Thu, 31 Jan 2019 21:14:50 +0100
Description: Do not build phylip plugin which is removed since
the code copy of the old version has no free license
=====================================
debian/patches/fix_desktop_file.patch
=====================================
@@ -0,0 +1,14 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Thu, 31 Jan 2019 21:14:50 +0100
+Description: Add exec code for mime in desktop file
+
+--- a/installer/_common_data/ugene.desktop
++++ b/installer/_common_data/ugene.desktop
+@@ -5,6 +5,6 @@ GenericName=Unipro UGENE
+ Terminal=false
+ Icon=ugene
+ Type=Application
+-Exec=ugene -ui
++Exec=ugene -ui %f
+ Categories=Education;Science;
+ MimeType=application/x-ugene-fa;application/x-ugene-uprj;application/x-ugene-uwl;application/x-ugene-uql;application/x-ugene-abi;application/x-ugene-aln;application/x-ugene-embl;application/x-ugene-sw;application/x-ugene-fastq;application/x-ugene-gb;application/x-ugene-gff;application/x-ugene-msf;application/x-ugene-newick;application/x-ugene-pdb;application/x-ugene-sam-bam;application/x-ugene-srfa;application/x-ugene-sto;application/x-ugene-db;application/x-ugene-scf;application/x-ugene-mmdb;application/x-ugene-hmm;
=====================================
debian/patches/series
=====================================
@@ -3,3 +3,4 @@ hardening.patch
debian_packaged_libs.patch
add_missing_header.patch
do_not_build_phylip.patch
+fix_desktop_file.patch
=====================================
debian/ugene-data.lintian-overrides deleted
=====================================
@@ -1,4 +0,0 @@
-# Suppress false positives since the package contains byte identical files taken over from upstream tarball
-ugene-data: package-contains-timestamped-gzip usr/share/ugene/data/sitecon_models/*/*.sitecon.gz
-ugene-data: package-contains-timestamped-gzip usr/share/ugene/data/enzymes/2013_08_01.bairoch.gz
-ugene-data: package-contains-timestamped-gzip usr/share/ugene/data/samples/CLUSTALW/ty3.aln.gz
=====================================
debian/ugene.install
=====================================
@@ -3,3 +3,4 @@ usr/lib/ugene
usr/share/applications
usr/share/pixmaps
usr/share/mime
+usr/share/icons
View it on GitLab: https://salsa.debian.org/med-team/ugene/compare/d0b128d7d258166e2176a756c611281c491195fb...2fb0ac5dd244cf1832f7f02a929826c6b6818739
--
View it on GitLab: https://salsa.debian.org/med-team/ugene/compare/d0b128d7d258166e2176a756c611281c491195fb...2fb0ac5dd244cf1832f7f02a929826c6b6818739
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