--- ugene-1.5.2+repack.orig/debian/changelog +++ ugene-1.5.2+repack/debian/changelog @@ -0,0 +1,58 @@ +ugene (1.5.2+repack-0ubuntu1) lucid; urgency=low + + * New upstream release LP: #486583 + * Bump standards-version to 3.8.3. No other changes. + + -- Bhavani Shankar Sun, 22 Nov 2009 14:46:07 +0530 + +ugene (1.5.1+repack-0ubuntu1) karmic; urgency=low + + * New upstream release LP: #405922 + * Bump standards-version to 3.8.2. No other changes. + + -- Bhavani Shankar Tue, 28 Jul 2009 22:55:13 +0530 + +ugene (1.5.0+repack-0ubuntu1) karmic; urgency=low + + * New upstream release + * Copyright information updated + * Versions of needed packages are bumped up + because of some bugs in older versions + * Closes LP: #397779 + + -- Ivan Efremov Tue, 07 Jul 2009 16:39:27 +0700 + +ugene (1.4.2+repack-0ubuntu1) karmic; urgency=low + + * New upstream release + + -- Morten Kjeldgaard Tue, 16 Jun 2009 13:20:00 +0200 + +ugene (1.4.1+repack-0ubuntu1) karmic; urgency=low + + * New upstream release. + * Bump-up Standards. + + -- Alessio Treglia Thu, 30 Apr 2009 08:14:03 +0200 + +ugene (1.3.3+repack-0ubuntu1) jaunty; urgency=low + + [ Bhavani Shankar ] + * New Upstream version (LP: #326830) + * Files unneeded for this package were removed from + the original tarball. + + [ Morten Kjeldgaard ] + * Fixed debian/watch to mangle local name + * Fixed get-orig-source rule to name repackaged tarball correctly. + * Copyright for two files specified. + + -- Bhavani Shankar Sun, 08 Feb 2009 16:32:24 +0530 + +ugene (1.3.2+repack-0ubuntu1) jaunty; urgency=low + + * Initial packaging (LP: #319917) + * Files unneeded for this package were removed from + the original tarball + + -- Ivan Efremov Mon, 26 Jan 2009 19:17:51 +0600 --- ugene-1.5.2+repack.orig/debian/watch +++ ugene-1.5.2+repack/debian/watch @@ -0,0 +1,4 @@ +version=3 +opts=dversionmangle=s/\+repack// \ +http://ugene.unipro.ru/download.html \ + downloads/ugene-([\d.]*)\.tar\.gz debian uupdate --- ugene-1.5.2+repack.orig/debian/compat +++ ugene-1.5.2+repack/debian/compat @@ -0,0 +1 @@ +5 --- ugene-1.5.2+repack.orig/debian/control +++ ugene-1.5.2+repack/debian/control @@ -0,0 +1,26 @@ +Source: ugene +Section: science +Priority: optional +Maintainer: Ubuntu Developers +XSBC-Original-Maintainer: Ivan Efremov +Build-Depends: libqt4-dev (>= 4.5.0), libqt4-opengl-dev (>= 4.5.0), zlib1g-dev, debhelper +Standards-Version: 3.8.3 +Homepage: http://ugene.unipro.ru + +Package: ugene +Architecture: any +Depends: ${shlibs:Depends}, libqt4-gui (>=4.5.0), libqt4-core (>=4.5.0), ugene-data +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. + +Package: ugene-data +Architecture: all +Description: required data for UGENE - integrated bioinformatics toolkit + Unipro UGENE is a cross-platform visual environment for DNA and protein + sequence analysis. + . + This package contains various data and example files for UGENE. --- ugene-1.5.2+repack.orig/debian/copyright +++ ugene-1.5.2+repack/debian/copyright @@ -0,0 +1,252 @@ +This package was debianized by Ivan Efremov on +Mon, 26 Jan 2009 19:18:51 +0600 + +It was downloaded from: http://ugene.unipro.ru/download.html + +Modifications to the original source package: + The following directories have been removed: + ./bkm + ./installer/linux + ./installer/macosx + ./installer/windows + ./src/libs_3rdparty/zlib + since they contain useless for this package data. + +Upstream Author: UniPro + +Copyright: + Copyright (C) 2008, 2009 by UniPro + +License: + This suite of programs is free software. You can redistribute it + and/or modify it under the terms of the GNU General Public License as + published by the Free Software Foundation; either version 2 of the + License, or (at your option) any later version. + + In other words, you are free to modify, copy, or redistribute this + source code and its documentation in any way you like, but you must + distribute all derivative versions as free software under the same + terms that I've provided my code to you (i.e. the GNU General Public + License). This precludes any use of the code in proprietary or + commercial software unless your source code is made freely available. + + If you wish to use Unipro UGENE code under a different Open Source + license that's not compatible with the GPL (like the Artistic License, BSD + license, or the Netscape Public License), please contact us + (ugene@unipro.ru) for permission. + + Incorporation into commercial software under non-GPL terms is possible + by obtaining a specially licensed version from Unipro. + Contact 'ugene@unipro.ru' to arrange licensing terms. + + This software is distributed in the hope that it will be useful, but + WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU + General Public License for more details. + + You should have received a copy of the GNU General Public License + along with this Unipro UGENE release, in the file LICENSE; + 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 + + +Files: src/core/src/document_format/IOLibsUtils.h + src/core/src/document_format/ABIFormat.cpp + src/core/src/document_format/SCFFormat.cpp +Copyright: 1994 Medical Research Council. All rights reserved. +License: + Permission to use, copy, modify and distribute this software and its + documentation for any purpose is hereby granted without fee, provided that + this copyright and notice appears in all copies. + + MRC disclaims all warranties with regard to this software. + + +The File src/libs_3rdparty/qtbindings_core/src/qtscriptconcurrent.h + Copyright (C) 1992-2008 Trolltech ASA + + Released under the terms of GPL (v2 or any later version). + (http://labs.trolltech.com/page/Projects/QtScript/Generator) + + +The Files in src/libs_3rdparty/qtbindings_core + src/libs_3rdparty/qtbindings_gui + src/libs_3rdparty/qtbindings_xml + + are automatically generated by Qt Script Generator + (http://labs.trolltech.com/page/Projects/QtScript/Generator) and have + the same license as the API they binds. Therefore, this files are + relased under the terms of GPL. + + +The File src/plugins_3rdparty/hmm2/src/hmmer2/sre_string.cpp + Copyright (c) 1998 Todd C. Miller + + Permission to use, copy, modify, and distribute this software for any + purpose with or without fee is hereby granted, provided that the above + copyright notice and this permission notice appear in all copies. + + THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES + WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF + MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR + ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES + WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN + ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF + OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. + + +The Files in src/plugins_3rdparty/hmm2 + HMMER - Biological sequence analysis with profile hidden Markov models + Copyright (C) 1992-2003 HHMI/Washington University School of Medicine + + This suite of programs is free software. You can redistribute it + and/or modify it under the terms of the GNU General Public License as + published by the Free Software Foundation; either version 2 of the + License, or (at your option) any later version. + + In other words, you are free to modify, copy, or redistribute this + source code and its documentation in any way you like, but you must + distribute all derivative versions as free software under the same + terms that I've provided my code to you (i.e. the GNU General Public + License). This precludes any use of the code in proprietary or + commercial software unless your source code is made freely available. + + If you wish to use HMMER code under a different Open Source license + that's not compatible with the GPL (like the Artistic License, BSD + license, or the Netscape Public License), please contact me + (eddy@genetics.wustl.edu) for permission. + + Incorporation into commercial software under non-GPL terms is possible + by obtaining a specially licensed version from Washington University + School of Medicine. Contact Jack Pincus (jhpincus@cris.com) to arrange + licensing terms. + + This software is distributed in the hope that it will be useful, but + WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU + General Public License for more details. + + You should have received a copy of the GNU General Public License + along with this HMMER release, in the file LICENSE; 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 + +Note: +The Files in src/plugins_3rdparty/uhmmer/src/u_spu and + src/plugins_3rdparty/uhmmer/src/uhmmsearch_cell.cpp + are modified sources from the HMMER-Cell project + (ftp://selab.janelia.org/pub/software/hmmer/contrib-2.3.2/HMMerCell_src_02272008.tar.gz) + + Original Copyright: 2008, International Business Machines Corporation + Authors: Kursad Albayraktaroglu, Jizhu Lu + + This files are released under the terms of GPL (v2 or any later version). + + +The Files in src/plugins_3rdparty/umuscle/src/muscle + are PUBLIC DOMAIN (see http://www.drive5.com/muscle/license.htm) + + +The Files in src/plugins_3rdparty/script_debuger/src/qtscriptdebug + Copyright (C) 2007-2008 Trolltech ASA. All rights reserved. + + This file is part of the Qt Script Debug project on Trolltech Labs. + + This file may be used under the terms of the GNU General Public + License version 2.0 as published by the Free Software Foundation + and appearing in the file LICENSE.GPL included in the packaging of + this file. + + This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE + WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. + + +The Files src/plugins_3rdparty/psipred/src/seq2mtx.cpp + src/plugins_3rdparty/psipred/src/sspred_avpred.cpp + src/plugins_3rdparty/psipred/src/sspred_hmulti.cpp + Copyright (C) 2000 D.T. Jones + These files are distributed under the terms of custom GPL-compatible + license. See src/plugins_3rdparty/psipred/src/license for details. + + +The Files in src/plugins_3rdparty/primer3/src/primer3_core + Copyright (c) 1996,1997,1998,1999,2000,2001,2004,2006,2007 + Whitehead Institute for Biomedical Research, Steve Rozen + (http://jura.wi.mit.edu/rozen), and Helen Skaletsky + All rights reserved. + + Redistribution and use in source and binary forms, with or without + modification, are permitted provided that the following conditions are + met: + + * Redistributions of source code must retain the above copyright + notice, this list of conditions and the following disclaimer. + * 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. + * Neither the names of the copyright holders nor 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, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR + A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT + OWNERS 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; 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. + + +The Files in src/plugins_3rdparty/hmm3/src/hmmer3 +(except files in src/plugins_3rdparty/hmm3/src/hmmer3/easel) + Copyright (C) 2009 Howard Hughes Medical Institute. + Other copyrights also apply. See the + 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). + + +The Files in src/plugins_3rdparty/hmm3/src/hmmer3/easel + Copyright (C) 2009 Howard Hughes Medical Institute. + Other copyrights also apply. See the + src/plugins_3rdparty/hmm3/src/hmmer3/easel/COPYRIGHT file for a full list. + + Easel is distributed under the Janelia Farm Software License, a BSD + license. See the src/plugins_3rdparty/hmm3/src/hmmer3/easel/LICENSE file + for more details. + + +The Files in src/plugins/biostruct3d_view/src/gl2ps + GL2PS, an OpenGL to PostScript Printing Library + Copyright (C) 1999-2006 Christophe Geuzaine + + This program is free software; you can redistribute it and/or + modify it under the terms of either: + + a) the GNU Library General Public License as published by the Free + Software Foundation, either version 2 of the License, or (at your + option) any later version; or + + b) the GL2PS License as published by Christophe Geuzaine, either + version 2 of the License, or (at your option) any later version. + + This program is distributed in the hope that it will be useful, but + WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See either + the GNU Library General Public License or the GL2PS License for + more details. + + +Packaging: + Copyright (C) 2008, 2009 by Ivan Efremov + released under the GPL. --- ugene-1.5.2+repack.orig/debian/rules +++ ugene-1.5.2+repack/debian/rules @@ -0,0 +1,77 @@ +#!/usr/bin/make -f + +export DH_OPTIONS + +UPSTREAM_NAME=ugene +UPSTREAM_VERSION=$(shell uscan --dehs | sed -n 's/.*\(.*\)<\/upstream-version>.*/\1/p') +UPSTREAM_FOLDER=$(UPSTREAM_NAME)-$(UPSTREAM_VERSION) + +get-orig-source: + uscan --force-download --no-symlink + tar -xzf ../$(UPSTREAM_NAME)-$(UPSTREAM_VERSION).tar.gz + rm -rf $(UPSTREAM_FOLDER)/bkm + rm -rf $(UPSTREAM_FOLDER)/installer/linux + rm -rf $(UPSTREAM_FOLDER)/installer/macosx + rm -rf $(UPSTREAM_FOLDER)/installer/windows + rm -rf $(UPSTREAM_FOLDER)/src/libs_3rdparty/zlib + GZIP="-9" tar -czf ../$(UPSTREAM_NAME)_$(UPSTREAM_VERSION)+repack.orig.tar.gz $(UPSTREAM_FOLDER) + rm -rf $(UPSTREAM_FOLDER) + + +build: build-arch build-indep + +build-arch: build-arch-stamp +build-arch-stamp: + qmake-qt4 -r + $(MAKE) + touch $@ + +build-indep: build-indep-stamp +build-indep-stamp: + touch $@ + +clean: + dh_testdir + dh_testroot + rm -f build-arch-stamp build-indep-stamp + [ ! -f Makefile ] || $(MAKE) distclean + dh_clean + +install: install-indep install-arch +install-indep: + dh_testdir + dh_testroot + dh_clean -k -i + dh_install -i data /usr/share/ugene + +install-arch: + dh_testdir + dh_testroot + dh_clean -k -s + dh_installdirs -s + + $(MAKE) INSTALL_ROOT=$$(pwd)/debian/ugene install + rm -rf debian/ugene/usr/share/ugene + +binary-common: + dh_testdir + dh_testroot + dh_installchangelogs debian/changelog + dh_installdocs + dh_strip + dh_compress + dh_fixperms + dh_installdeb + export LD_LIBRARY_PATH=$$(pwd)/debian/ugene/usr/lib/ugene && dh_shlibdeps + dh_gencontrol + dh_md5sums + dh_builddeb + +binary-indep: build-indep install-indep + $(MAKE) -f debian/rules DH_OPTIONS=-i binary-common + +binary-arch: build-arch install-arch + $(MAKE) -f debian/rules DH_OPTIONS=-s binary-common + +binary: binary-arch binary-indep +.PHONY: build clean binary-indep binary-arch binary install install-indep install-arch