[med-svn] r8401 - trunk/packages/ugene/trunk/debian

Thu Nov 3 12:38:16 UTC 2011

Author: moeller
Date: 2011-11-03 12:38:16 +0000 (Thu, 03 Nov 2011)
New Revision: 8401

Added:
   trunk/packages/ugene/trunk/debian/README.Debian
   trunk/packages/ugene/trunk/debian/ugene.lintian-overrides
Modified:
   trunk/packages/ugene/trunk/debian/changelog
   trunk/packages/ugene/trunk/debian/control
   trunk/packages/ugene/trunk/debian/copyright
   trunk/packages/ugene/trunk/debian/rules
Log:
First upload of ugene to experimental.


Added: trunk/packages/ugene/trunk/debian/README.Debian
===================================================================

--- trunk/packages/ugene/trunk/debian/README.Debian	                        (rev 0)
+++ trunk/packages/ugene/trunk/debian/README.Debian	2011-11-03 12:38:16 UTC (rev 8401)
@@ -0,0 +1,20 @@
+ugene for Debian and Ubuntu
+===========================
+
+UGENE is great to have around. It was first released to Ubuntu.
+This package took the sources from upstream's Ubuntu PPA and
+recompiled on Debian.
+
+The upstream developer has done all the Debian packaging himself
+and has commit privileges to the Debian Med SCM. It will be
+interesting to see this package, which in term of functionality
+has quite a character of a Meta-Package, will develop with
+helping hands of the distribution.
+
+The package has a series of source code redundancies with packages
+that Debian is already shipping. We need to work on those a bit
+for the package to leave experimental.
+
+Steffen - the sponsor
+
+-- Wed Nov  2 13:42:11 CET 2011

Modified: trunk/packages/ugene/trunk/debian/changelog
===================================================================
--- trunk/packages/ugene/trunk/debian/changelog	2011-11-03 10:00:00 UTC (rev 8400)
+++ trunk/packages/ugene/trunk/debian/changelog	2011-11-03 12:38:16 UTC (rev 8401)
@@ -1,3 +1,13 @@
+ugene (1.9.8+repack-1) experimental; urgency=low
+
+  * First release to Debian
+    - added README.Debian
+    - increased policy version to 3.9.2
+    - added URLs for version control system
+  * Added debug package.
+
+ -- Steffen Moeller <moeller at debian.org>  Wed, 02 Nov 2011 13:29:07 +0100
+
 ugene (1.9.8+repack-0ubuntu1~oneiric) oneiric; urgency=low
 
   * Latest release oneiric build
@@ -79,8 +89,9 @@
 
   * New upstream release
   * Copyright information updated
- -- Konstantin Okonechnikov <k.okonechnikov at gmail>   Tue, 7 Apr 2009 00:15:00 +0600
 
+ -- Konstantin Okonechnikov <k.okonechnikov at gmail.com>  Tue, 7 Apr 2009 00:15:00 +0600
+
 ugene (1.5.2+repack-0ubuntu1) karmic; urgency=low
 
   * New upstream release

Modified: trunk/packages/ugene/trunk/debian/control
===================================================================
--- trunk/packages/ugene/trunk/debian/control	2011-11-03 10:00:00 UTC (rev 8400)
+++ trunk/packages/ugene/trunk/debian/control	2011-11-03 12:38:16 UTC (rev 8401)
@@ -1,11 +1,13 @@
 Source: ugene
 Section: science
 Priority: optional
-Maintainer: Ubuntu Developers <ubuntu-devel-discuss at lists.ubuntu.com>
-XSBC-Original-Maintainer: Ivan Efremov <iefremov at unipro.ru> 
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Ivan Efremov <iefremov at unipro.ru>, Steffen Moeller <moeller at debian.org>
 Build-Depends: libqt4-dev (>= 4.7.0), libqtwebkit-dev, libqt4-opengl-dev (>= 4.7.0), zlib1g-dev, debhelper (>=5.0.38)
-Standards-Version: 3.9.1
+Standards-Version: 3.9.2
 Homepage: http://ugene.unipro.ru
+Vcs-svn: svn://svn.debian.org/svn/debian-med/trunk/packages/ugene/trunk
+Vcs-browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/ugene/trunk/
 
 Package: ugene
 Architecture: any
@@ -25,3 +27,20 @@
  sequence analysis. 
  .
  This package contains various data and example files for UGENE. 
+
+Package: ugene-dbg
+Architecture: any
+Priority: extra
+Section: debug
+Depends: ${misc:Depends}, ugene (= ${binary:Version})
+Description: integrated bioinformatics toolkit
+ 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.
+ .
+ This package provides symbols stripped from the regular binaries to
+ help with further information during debug sessions. You may be asked
+ to install this package to help localising a bug you reported to
+ the developers.

Modified: trunk/packages/ugene/trunk/debian/copyright
===================================================================
--- trunk/packages/ugene/trunk/debian/copyright	2011-11-03 10:00:00 UTC (rev 8400)
+++ trunk/packages/ugene/trunk/debian/copyright	2011-11-03 12:38:16 UTC (rev 8401)
@@ -48,7 +48,8 @@
     if not, write to the Free Software Foundation, Inc.,
     51 Franklin St, Fifth Floor, Boston, MA 02110-1301, USA.
 
-    See /usr/share/common-licenses/GPL for the complete text of the GPL
+    On Debian systems, see /usr/share/common-licenses/GPL-2 for the complete
+    text of the GPL.
 
 
 Files: src/corelibs/U2Formats/src/ABIFormat.cpp
@@ -115,7 +116,8 @@
     the Free Software Foundation, Inc.,
     51 Franklin St, Fifth Floor, Boston, MA 02110-1301, USA.
                                                 
-    See /usr/share/common-licenses/GPL for the complete text of the GPL
+    On Debian systems, see /usr/share/common-licenses/GPL-2 for the
+    complete text of the GPL.
 
 Note:
 The Files in src/plugins_3rdparty/uhmmer/src/u_spu and 
@@ -181,7 +183,9 @@
     src/plugins_3rdparty/hmm3/src/hmmer3/COPYRIGHT file for a full list.
  
     HMMER is distributed under the terms of the GNU General Public License
-    (GPLv3).
+    (GPLv3). On Debian systems, see /usr/share/common-licenses/GPL-3 for
+    the full text of the license.
+   
 
 
 The Files in src/plugins_3rdparty/hmm3/src/hmmer3/easel
@@ -193,7 +197,10 @@
     license. See the src/plugins_3rdparty/hmm3/src/hmmer3/easel/LICENSE file 
     for more details.
 
+    On Debian systems, see /usr/share/common-licenses/BSD for the full
+    text of the license.
 
+
 The Files in src/plugins/biostruct3d_view/src/gl2ps
     GL2PS, an OpenGL to PostScript Printing Library
     Copyright (C) 1999-2006 Christophe Geuzaine <geuz at geuz.org>
@@ -213,6 +220,9 @@
     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See either
     the GNU Library General Public License or the GL2PS License for
     more details.
+
+    On Debian systems, see /usr/share/common-licenses/GPL-2 for the
+    full text of the GPL version 2.
    
 
 The Files in src/plugins_3rdparty/ball/include and
@@ -230,7 +240,10 @@
    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
    Lesser General Public License for more details.   
 
+   On Debian systems, see /usr/share/common-licenses/LGPL-2 for the
+   full text of the license.
 
+
 The Files in src/plugins_3rdparty/phylyp/src
    version 3.6. (c) Copyright 1993-2004 by the University of Washington.
    Written by Joseph Felsenstein, Akiko Fuseki, Sean Lamont, and Andrew Keeffe.
@@ -256,12 +269,16 @@
 
     You should have received a copy of the GNU General Public License
     along with this program; if not, write to the Free Software
-    Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
+    Foundation, Inc., 51 Franklin Street, Fifth Floor,
+    Boston, MA 02110-1301 USA
 
     Please send bug reports, comments etc. to:
     timolassmann at gmail.com
 
+    On Debian systems, see /usr/share/common-licenses/GPL-2 for the 
+    full text of the license.  
 
+
 The Files in src/plugins_3rdparty/bowtie/src/bowtie/SeqAn-1.1
     Copyright (C) 2007
 
@@ -275,7 +292,10 @@
     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
     Lesser General Public License for more details.
 
+    On Debian systems, see /usr/share/common-licenses/GPL-3 for the 
+    full text of the license.  
 
+
 The Files in src/plugins_3rdparty/bowtie/src/bowtie/visualstudio
     ISO C9x  compliant inttypes.h for Microsoft Visual Studio
     Based on ISO/IEC 9899:TC2 Committee draft (May 6, 2005) WG14/N1124 
@@ -374,8 +394,8 @@
     SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 
 
-
-
-Packaging:
+Files: debian/*
+License:
     Copyright (C) 2008-2011 by Ivan Efremov <iefremov at unipro.ru>
-    released under the GPL.
+    released under the GPL. On Debian systems, see 
+    /usr/share/common-licenses/GPL-3 for the full text of the license.

Modified: trunk/packages/ugene/trunk/debian/rules
===================================================================
--- trunk/packages/ugene/trunk/debian/rules	2011-11-03 10:00:00 UTC (rev 8400)
+++ trunk/packages/ugene/trunk/debian/rules	2011-11-03 12:38:16 UTC (rev 8401)
@@ -57,7 +57,8 @@
 	dh_testroot
 	dh_installchangelogs debian/changelog
 	dh_installdocs
-	dh_strip
+	dh_strip --dbg-package=ugene-dbg
+	dh_lintian
 	dh_compress
 	dh_fixperms
 	dh_installdeb

Added: trunk/packages/ugene/trunk/debian/ugene.lintian-overrides
===================================================================
--- trunk/packages/ugene/trunk/debian/ugene.lintian-overrides	                        (rev 0)
+++ trunk/packages/ugene/trunk/debian/ugene.lintian-overrides	2011-11-03 12:38:16 UTC (rev 8401)
@@ -0,0 +1,4 @@
+# For this first upload to experimental the build instructions were not
+# touched but will be communicated further with upstream.
+ugene binary: embedded-library usr/lib64/ugene/libugenedb.so.1.0.0: sqlite
+


