debian/0000775000000000000000000000000012032577732007200 5ustar debian/copyright0000664000000000000000000003672711654530362011147 0ustar 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: ./installer/linux ./installer/macosx ./installer/windows ./src/libs_3rdparty/zlib ./src/libs_3rdparty/sqlite3 since they contain useless for this package data. Upstream Author: UniPro Copyright: Copyright (C) 2008-2011 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/corelibs/U2Formats/src/ABIFormat.cpp src/corelibs/U2Formats/src/SCFFormat.cpp src/corelibs/U2Formats/src/IOLibUtils.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/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 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. The Files in src/plugins_3rdparty/ball/include and src/plugins_3rdparty/ball/source Copyright (C) Oliver Kohlbacher, Hans-Peter Lenhof, Andreas Hildebrandt and others 1996-2009 This library is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. This library 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 Lesser General Public License for more details. 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. Permission is granted to copy and use this program provided no fee is charged for it and provided that this copyright notice is not removed. The Files in src/plugins_3rdparty/kalign/src Released under GPL - see the 'COPYING' file Copyright (C) 2006 Timo Lassmann This program 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 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 the GNU General Public License for more details. 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 Please send bug reports, comments etc. to: timolassmann@gmail.com The Files in src/plugins_3rdparty/bowtie/src/bowtie/SeqAn-1.1 Copyright (C) 2007 This library is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 3 of the License, or (at your option) any later version. This library 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 Lesser General Public License for more details. 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 Copyright (c) 2006 Alexander Chemeris 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. The name of the author may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE AUTHOR ``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 AUTHOR 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/bowtie/src/bowtie This files are distributed under Artistic License. See the 'COPYING' file for details. The Files src/include/opencl/legacy/cl.h src/include/opencl/legacy/cl_platform.h Copyright (c) 2008-2010 The Khronos Group Inc. Permission is hereby granted, free of charge, to any person obtaining a copy of this software and/or associated documentation files (the "Materials"), to deal in the Materials without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Materials, and to permit persons to whom the Materials are furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Materials. THE MATERIALS ARE PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE MATERIALS OR THE USE OR OTHER DEALINGS IN THE MATERIALS. Packaging: Copyright (C) 2008-2011 by Ivan Efremov released under the GPL. debian/changelog0000664000000000000000000001076412032577732011062 0ustar ugene (1.9.8+repack-0ubuntu4) quantal; urgency=low * Fix build failure with GCC 4.7. -- Matthias Klose Tue, 02 Oct 2012 16:52:42 +0200 ugene (1.9.8+repack-0ubuntu3) precise; urgency=low * Fix brace mismatch in gles-disable-biostruct3d_view.patch. -- Colin Watson Fri, 20 Apr 2012 19:38:14 +0100 ugene (1.9.8+repack-0ubuntu2) precise; urgency=low * Cast floating literals to qreal before passing to qMin/qMax, since qreal is a float at least on ARM. * Include in a few places (LP: #935476). * Disable biostruct3d_view plugin when using GLES. -- Colin Watson Fri, 20 Apr 2012 15:12:23 +0100 ugene (1.9.8+repack-0ubuntu1) precise; urgency=low * New upstream release (LP: #820903). * Use system sqlite3 instead of bundled copy. * Drop dummy packages from Depends. * debian/rules: pass build flags from the environment. * Don't install Debian changelog twice. * Update watch file. * Bump Standards-Version to 3.9.2. -- Ilya Barygin Thu, 03 Nov 2011 19:05:28 +0400 ugene (1.9.1+repack-0ubuntu1) natty; urgency=low * New upstream release * Copyright information update * Bump version of Qt dependecy due to upstream reasons -- Ivan Efremov Thu, 10 Feb 2011 18:36:18 +0600 ugene (1.7.2+repack-0ubuntu1) natty; urgency=low * New upstream release * debian/rules: + Delete bkm directory removal rule from get-orig-source as its non-existent now * Bump standards-version to 3.9.1. No other changes. -- Bhavani Shankar Sat, 16 Oct 2010 14:33:07 +0530 ugene (1.7.1+repack-0ubuntu2) maverick; urgency=low * Build depend on libqtwebkit-dev instead of libqt4-webkit-dev since it is NBS -- Scott Kitterman Fri, 13 Aug 2010 13:05:01 -0400 ugene (1.7.1+repack-0ubuntu1) maverick; urgency=low * New upstream release (LP: #606642) * Switch to 3.0 (quilt) format * Bump standards-version to 3.9.0. No other changes. * Add ${misc:Depends} macro to Depends field (W: lintian) * Add versioned dependency on debhelper (W: lintian) * Casting fix dropped, fixed upstream. -- Bhavani Shankar Sat, 17 Jul 2010 19:31:43 +0530 ugene (1.7.0+repack-0ubuntu2) maverick; urgency=low * Casting fix for arm; double is not same as qreal. (LP: #600820) -- David Sugar Thu, 01 Jul 2010 17:08:15 +0000 ugene (1.7.0+repack-0ubuntu1) maverick; urgency=low * New upstream release. * debian/control: - Bump standards-version to 3.8.4. No other changes. - Add libqt4-webkit-dev to build-depends. * Update debian/copyright. -- Andreas Wenning Mon, 24 May 2010 15:19:27 +0200 ugene (1.5.2+repack-0ubuntu1) lucid; urgency=low * New upstream release LP: #486583 * Bump standards-version to 3.8.3. No other changes. * Update debian/copyright as per Ivan's suggestion. -- Bhavani Shankar Sun, 22 Nov 2009 15:20:16 +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 debian/source/0000775000000000000000000000000011525247647010505 5ustar debian/source/format0000664000000000000000000000001311525247647011712 0ustar 3.0 (quilt)debian/compat0000664000000000000000000000000211525247570010376 0ustar 5 debian/control0000664000000000000000000000234311654525415010605 0ustar Source: ugene Section: science Priority: optional Maintainer: Ubuntu Developers XSBC-Original-Maintainer: Ivan Efremov Build-Depends: libqt4-dev (>= 4.7.0), libqtwebkit-dev, libqt4-opengl-dev (>= 4.7.0), zlib1g-dev, libsqlite3-dev, debhelper (>= 5.0.38) Standards-Version: 3.9.2 Homepage: http://ugene.unipro.ru Package: ugene Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends}, 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 Depends: ${misc:Depends} 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. debian/watch0000664000000000000000000000023111654501357010224 0ustar version=3 opts=dversionmangle=s/\+repack// \ http://ugene.unipro.ru/downloads/ugene_get_latest_source.html \ .*/ugene-([\d.]*)\.tar\.gz debian uupdate debian/patches/0000775000000000000000000000000012032577667010636 5ustar debian/patches/glu-includes.patch0000664000000000000000000000245111744267055014250 0ustar Description: Include in a few places Author: Colin Watson Bug-Ubuntu: https://bugs.launchpad.net/bugs/935476 Forwarded: no Last-Update: 2012-04-20 Index: b/src/plugins/biostruct3d_view/src/AnaglyphRenderer.h =================================================================== --- a/src/plugins/biostruct3d_view/src/AnaglyphRenderer.h +++ b/src/plugins/biostruct3d_view/src/AnaglyphRenderer.h @@ -27,6 +27,8 @@ #include #include +#include + namespace U2 { class BioStruct3DGLWidget; Index: b/src/plugins/biostruct3d_view/src/GLFrameManager.cpp =================================================================== --- a/src/plugins/biostruct3d_view/src/GLFrameManager.cpp +++ b/src/plugins/biostruct3d_view/src/GLFrameManager.cpp @@ -24,6 +24,8 @@ #include "GLFrameManager.h" #include +#include + namespace U2 { const GLfloat GLFrame::DEFAULT_ZOOM = 45.0f; Index: b/src/plugins/biostruct3d_view/src/GraphicUtils.h =================================================================== --- a/src/plugins/biostruct3d_view/src/GraphicUtils.h +++ b/src/plugins/biostruct3d_view/src/GraphicUtils.h @@ -26,6 +26,8 @@ #include #include +#include + class GLUquadric; namespace U2 { debian/patches/system-sqlite.patch0000664000000000000000000000537211654516357014507 0ustar Description: use system libsqlite3 instead of bundled copy Author: Ilya Barygin --- ugene-1.9.8+repack.orig/ugene.pro +++ ugene-1.9.8+repack/ugene.pro @@ -8,7 +8,6 @@ SUBDIRS += \ src/libs_3rdparty/qscore \ - src/libs_3rdparty/sqlite3 \ src/libs_3rdparty/gtest \ src/corelibs/U2Core \ src/corelibs/U2Test \ --- ugene-1.9.8+repack.orig/src/plugins/dbi_sqlite/dbi_sqlite.pri +++ ugene-1.9.8+repack/src/plugins/dbi_sqlite/dbi_sqlite.pri @@ -4,7 +4,7 @@ PLUGIN_NAME=SQLite based DBI implementation PLUGIN_VENDOR=Unipro -LIBS += -lugenedb +LIBS += -lsqlite3 !debug_and_release|build_pass { @@ -16,5 +16,3 @@ include( ../../ugene_plugin_common.pri ) - -INCLUDEPATH += ../../libs_3rdparty/sqlite3/src \ No newline at end of file --- ugene-1.9.8+repack.orig/src/plugins/dbi_bam/dbi_bam.pri +++ ugene-1.9.8+repack/src/plugins/dbi_bam/dbi_bam.pri @@ -10,7 +10,7 @@ INCLUDEPATH += ../../libs_3rdparty/zlib/src } -LIBS += -lugenedb +LIBS += -lsqlite3 !debug_and_release|build_pass { @@ -19,5 +19,3 @@ LIBS += -lugenedbd } } - -INCLUDEPATH += ../../libs_3rdparty/sqlite3/src --- ugene-1.9.8+repack.orig/src/corelibs/U2Core/U2Core.pri +++ ugene-1.9.8+repack/src/corelibs/U2Core/U2Core.pri @@ -15,9 +15,7 @@ } LIBS += -L../../_release -LIBS += -lugenedb - -INCLUDEPATH += ../../libs_3rdparty/sqlite3/src +LIBS += -lsqlite3 !debug_and_release|build_pass { --- ugene-1.9.8+repack.orig/src/ugenecl/ugenecl.pri +++ ugene-1.9.8+repack/src/ugenecl/ugenecl.pri @@ -9,7 +9,7 @@ DEFINES+= QT_DLL QT_FATAL_ASSERT INCLUDEPATH += src _tmp ../include ../corelibs/U2Private/src -LIBS += -L../_release -lU2Core -lU2Algorithm -lU2Formats -lU2Gui -lU2Test -lU2Remote -lU2Misc -lU2Lang -lU2Private -lugenedb +LIBS += -L../_release -lU2Core -lU2Algorithm -lU2Formats -lU2Gui -lU2Test -lU2Remote -lU2Misc -lU2Lang -lU2Private -lsqlite3 !debug_and_release|build_pass { --- ugene-1.9.8+repack.orig/src/ugeneui/ugeneui.pri +++ ugene-1.9.8+repack/src/ugeneui/ugeneui.pri @@ -9,7 +9,7 @@ DEFINES+= QT_DLL QT_FATAL_ASSERT INCLUDEPATH += src _tmp ../include ../corelibs/U2Private/src -LIBS += -L../_release -lU2Core -lU2Algorithm -lU2Formats -lU2Gui -lU2View -lU2Test -lU2Remote -lU2Misc -lU2Lang -lU2Private -lugenedb +LIBS += -L../_release -lU2Core -lU2Algorithm -lU2Formats -lU2Gui -lU2View -lU2Test -lU2Remote -lU2Misc -lU2Lang -lU2Private -lsqlite3 !debug_and_release|build_pass { --- ugene-1.9.8+repack.orig/src/plugins/dbi_file/dbi_file.pri +++ ugene-1.9.8+repack/src/plugins/dbi_file/dbi_file.pri @@ -4,7 +4,7 @@ PLUGIN_NAME=DBI implementation based on local files PLUGIN_VENDOR=Unipro -LIBS += -lugenedb +LIBS += -lsqlite3 !debug_and_release|build_pass { debian/patches/qreal.patch0000664000000000000000000000307011744253750012754 0ustar Description: Cast floating literals to qreal before passing to qMin/qMax Floating literals are doubles by default, but qreal is a float at least on ARM. Author: Colin Watson Forwarded: no Last-Update: 2012-04-20 Index: b/src/corelibs/U2View/src/util_ov_phyltree/TreeViewer.cpp =================================================================== --- a/src/corelibs/U2View/src/util_ov_phyltree/TreeViewer.cpp +++ b/src/corelibs/U2View/src/util_ov_phyltree/TreeViewer.cpp @@ -530,7 +530,7 @@ } } - qreal coef = qMax(1.0, TreeViewerUI::SIZE_COEF*treeSettings.width_coef); + qreal coef = qMax(qreal(1.0), TreeViewerUI::SIZE_COEF*treeSettings.width_coef); switch (treeSettings.type) { @@ -669,7 +669,7 @@ } newzoom = zoom * newzoom; newzoom = qMax(MINIMUM_ZOOM, newzoom); - newzoom = qMin(MAXIMUM_ZOOM * qMax(treeSettings.width_coef*TreeViewerUI::SIZE_COEF, 1.0), newzoom); + newzoom = qMin(MAXIMUM_ZOOM * qMax(treeSettings.width_coef*TreeViewerUI::SIZE_COEF, qreal(1.0)), newzoom); scale(newzoom / zoom, newzoom / zoom); zoom = newzoom; updateActionsState(); @@ -1141,7 +1141,7 @@ void TreeViewerUI::updateActionsState(){ - zoomToAction->setEnabled(zoom < MAXIMUM_ZOOM* qMax(treeSettings.width_coef*TreeViewerUI::SIZE_COEF, 1.0)); + zoomToAction->setEnabled(zoom < MAXIMUM_ZOOM* qMax(treeSettings.width_coef*TreeViewerUI::SIZE_COEF, qreal(1.0))); zoomOutAction->setEnabled(zoom > MINIMUM_ZOOM); if(isSelectedCollapsed()){ debian/patches/fix-ftbfs-4.7.diff0000664000000000000000000000213112032577667013663 0ustar Index: ugene-1.9.8+repack/src/plugins_3rdparty/bowtie/src/bowtie/alphabet.h =================================================================== --- ugene-1.9.8+repack.orig/src/plugins_3rdparty/bowtie/src/bowtie/alphabet.h 2011-10-25 14:33:58.000000000 +0000 +++ ugene-1.9.8+repack/src/plugins_3rdparty/bowtie/src/bowtie/alphabet.h 2012-10-02 14:52:35.348971248 +0000 @@ -39,6 +39,18 @@ return s_rc; } +/// Reverse a string in-place +template +static inline void reverseInPlace(TStr& s) { + typedef typename Value::Type TVal; + size_t len = length(s); + for(size_t i = 0; i < (len>>1); i++) { + TVal tmp = s[i]; + s[i] = s[len-i-1]; + s[len-i-1] = tmp; + } +} + /** * Reverse-complement s in-place. Ns go to Ns. */ @@ -70,18 +82,6 @@ } } -/// Reverse a string in-place -template -static inline void reverseInPlace(TStr& s) { - typedef typename Value::Type TVal; - size_t len = length(s); - for(size_t i = 0; i < (len>>1); i++) { - TVal tmp = s[i]; - s[i] = s[len-i-1]; - s[len-i-1] = tmp; - } -} - /** * Return the reverse-complement of s. */ debian/patches/series0000664000000000000000000000015212032577527012044 0ustar system-sqlite.patch qreal.patch glu-includes.patch gles-disable-biostruct3d_view.patch fix-ftbfs-4.7.diff debian/patches/gles-disable-biostruct3d_view.patch0000664000000000000000000000147311744326402017500 0ustar Description: Disable biostruct3d_view plugin when using GLES It has too many OpenGL dependencies at the moment, and needs porting. Author: Colin Watson Forwarded: no Last-Update: 2012-04-20 Index: b/ugene.pro =================================================================== --- a/ugene.pro +++ b/ugene.pro @@ -33,8 +33,13 @@ src/plugins_3rdparty/phylip \ src/plugins_3rdparty/kalign \ src/plugins_3rdparty/ptools \ - src/plugins/assembly_browser \ - src/plugins/biostruct3d_view \ + src/plugins/assembly_browser + +!contains(QT_CONFIG, opengles.*) { + SUBDIRS += src/plugins/biostruct3d_view +} + +SUBDIRS += \ src/plugins/chroma_view \ src/plugins/circular_view \ src/plugins/annotator \ debian/rules0000775000000000000000000000364211654532462010265 0ustar #!/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)/installer/linux rm -rf $(UPSTREAM_FOLDER)/installer/macosx rm -rf $(UPSTREAM_FOLDER)/installer/windows rm -rf $(UPSTREAM_FOLDER)/src/libs_3rdparty/zlib rm -rf $(UPSTREAM_FOLDER)/src/libs_3rdparty/sqlite3 GZIP="-9" tar -czf ../$(UPSTREAM_NAME)_$(UPSTREAM_VERSION)+repack.orig.tar.gz $(UPSTREAM_FOLDER) rm -rf $(UPSTREAM_FOLDER) build: build-arch build-indep build-arch: build-arch-stamp build-arch-stamp: qmake-qt4 -r "QMAKE_CXXFLAGS=$(CPPFLAGS) $(CXXFLAGS)" "QMAKE_LFLAGS=$(LDFLAGS)" $(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_prep -i dh_install -i -Xdata/license data /usr/share/ugene install-arch: dh_testdir dh_testroot dh_prep -a dh_installdirs -a $(MAKE) INSTALL_ROOT=$$(pwd)/debian/ugene install rm -rf debian/ugene/usr/share/ugene binary-common: dh_testdir dh_testroot dh_installchangelogs dh_installdocs dh_strip dh_compress dh_fixperms dh_installdeb export LD_LIBRARY_PATH=$$(pwd)/debian/ugene/usr/lib/ugene:$$(pwd)/debian/ugene/usr/lib64/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