.gitignore

@@ -2,6 +2,8 @@
 **/_tmp
 src/_debug
 src/_release
+src/qmake_msvc_proj_x32.cmd
+src/qmake_msvc_proj_x64.cmd
 
 # Makefiles generated by qmake
 Makefile
@@ -16,7 +18,8 @@ Makefile.Debug
 # Doxygen generated files
 /html
 
-# VS project files
+# VS project files and directories
+/.vs/
 *.sdf
 *.opensdf
 *.suo
@@ -31,8 +34,7 @@ Makefile.Debug
 
 # Windows generated files
 *.obj
-**/Win32/Debug/*
-ugene.VC.db
+*moc_predefs.h*ugene.VC.db
 ugene.VC.VC.opendb
 
 # Generated ugene shell launcher

.gitmodules

-[submodule "QSpec"]
-	path = src/libs_3rdparty/QSpec
-	url = https://github.com/ugeneunipro/QSpec.git
-	branch = ugene
-	ignore = dirty
\ No newline at end of file

README.md

@@ -4,7 +4,7 @@
 
 ### Prerequisites
 
-Make sure the Qt (>= 5.2.1 and < 5.6) development libraries are installed:
+Make sure the Qt (>= 5.3.2) development libraries are installed:
 
 * Ubuntu >=14.04: `sudo apt-get install qt5-default qttools5-dev-tools qtscript5-dev libqt5svg5-dev libqt5webkit5-dev`
 * Ubuntu 12.04:

data/workflow_samples/NGS/fastqc.uwl

@@ -8,7 +8,6 @@ workflow "Quality control by FastQC"{
     fastqc {
         type:fastqc;
         name:"FastQC Quality Control";
-        out-mode:1;
     }
     get-file-list {
         type:get-file-list;
@@ -29,8 +28,8 @@ workflow "Quality control by FastQC"{
             fastqc.contaminants {
                 alias:c;
             }
-            fastqc.custom-dir {
-                alias:out_dir;
+            fastqc.out-file {
+                alias:out_file;
             }
             fastqc.out-mode {
                 alias:mode;
@@ -41,13 +40,13 @@ workflow "Quality control by FastQC"{
         }
         visual {
             fastqc {
-                pos:"-493 -559";
+                pos:"-480 -540";
                 style:ext;
                 bg-color-ext:"0 128 64 64";
                 in-file.angle:180;
             }
             get-file-list {
-                pos:"-773 -560";
+                pos:"-765 -540";
                 style:ext;
                 bg-color-ext:"216 113 57 64";
                 bounds:"-30 -30 116.25 84";
@@ -59,7 +58,6 @@ workflow "Quality control by FastQC"{
         }
         wizard {
             name:"Quality Control by FastQC Wizard";
-            help-page-id:16122729;
             auto-run:true;
             page {
                 id:1;

data/workflow_samples/NGS/from_tools_menu_only/ngs_classification.uwl

@@ -32,7 +32,7 @@ workflow "NGS reads classification" {
                             value {
                                 id: parallel;
                                 label: "Parallel reads classification";
-                                tooltip:"Improve reads quality with Trimmomatic, classify them with Kraken, CLARK and in case of single-end reads with DIAMOND. Join the classification output with WEVOTE.";
+                                tooltip:"Improve reads quality with Trimmomatic, classify them with Kraken, CLARK, DIAMOND (in case of single-end reads), and MetaPhlAn2. Compare output from Kraken, CLARK, and DIAMOND with WEVOTE.";
                             }
                             value {
                                 id: de_novo;

data/workflow_samples/NGS/ngs_classification/ngs_classification_de_novo/ngs_classification_de_novo_single.uwl

@@ -55,6 +55,14 @@ workflow "SE reads assembly and classification"{
     get-se-reads-list.reads-url1->trimmomatic.in.reads-url1
 
     .meta {
+        parameter-aliases {
+            get-se-reads-list.url1 {
+                alias:in;
+            }
+            trimmomatic.trimming-steps {
+                alias:steps;
+            }
+        }
         visual {
             classification-report {
                 pos:"-465 -300";

data/workflow_samples/NGS/ngs_classification/ngs_classification_parallel/ngs_classification_parallel_paired.uwl

@@ -57,19 +57,25 @@ workflow "Parallel classification for PE reads"{
         name:Trimmomatic;
         input-data:paired-end;
     }
+    metaphlan2-classify {
+        type:metaphlan2-classify;
+        name:MetaPhlAn2;
+        input-data:paired-end;
+    }
 
     .actor-bindings {
+        get-pe-reads-list.out->fastqc-before-1.in-file
+        get-pe-reads-list.out->fastqc-before-2.in-file
+        get-pe-reads-list.out->trimmomatic.in
+        kraken-classify.out->ensemble-classification.tax-data1
+        ensemble-classification.out->wevote-classify.in
+        clark-classify.out->ensemble-classification.tax-data2
         wevote-classify.out->classification-report.in
         trimmomatic.out->fastqc-after-1.in-file
         trimmomatic.out->fastqc-after-2.in-file
         trimmomatic.out->kraken-classify.in
         trimmomatic.out->clark-classify.in
-        kraken-classify.out->ensemble-classification.tax-data1
-        clark-classify.out->ensemble-classification.tax-data2
-        ensemble-classification.out->wevote-classify.in
-        get-pe-reads-list.out->fastqc-before-1.in-file
-        get-pe-reads-list.out->fastqc-before-2.in-file
-        get-pe-reads-list.out->trimmomatic.in
+        trimmomatic.out->metaphlan2-classify.in
     }
 
     get-pe-reads-list.reads-url1->fastqc-before-1.in-file.url
@@ -86,77 +92,85 @@ workflow "Parallel classification for PE reads"{
     wevote-classify.tax-data->classification-report.in.tax-data
     get-pe-reads-list.reads-url1->trimmomatic.in.reads-url1
     get-pe-reads-list.reads-url2->trimmomatic.in.reads-url2
+    trimmomatic.reads-url1->metaphlan2-classify.in.reads-url1
+    trimmomatic.reads-url2->metaphlan2-classify.in.reads-url2
 
     .meta {
         visual {
             clark-classify {
-                pos:"-255 -435";
+                pos:"-315 -420";
                 style:simple;
                 bg-color-simple:"0 145 0 255";
                 in.angle:99.7276;
                 out.angle:291.541;
             }
             classification-report {
-                pos:"-600 -285";
+                pos:"-585 -270";
                 style:simple;
                 bg-color-simple:"141 126 194 255";
                 in.angle:345.964;
             }
             ensemble-classification {
-                pos:"-165 -285";
+                pos:"-150 -270";
                 style:simple;
                 bg-color-simple:"102 102 102 255";
                 out.angle:186.911;
-                tax-data1.angle:53.427;
+                tax-data1.angle:90;
                 tax-data2.angle:128.66;
                 tax-data3.angle:225;
             }
             fastqc-after-1 {
-                pos:"-165 -705";
+                pos:"-150 -690";
                 style:simple;
                 bg-color-simple:"81 120 78 255";
                 in-file.angle:236.31;
             }
             fastqc-after-2 {
-                pos:"-60 -705";
+                pos:"-45 -690";
                 style:simple;
                 bg-color-simple:"81 120 78 255";
                 in-file.angle:212.471;
             }
             fastqc-before-1 {
-                pos:"-480 -705";
+                pos:"-465 -690";
                 style:simple;
                 bg-color-simple:"81 120 78 255";
                 in-file.angle:233.842;
             }
             fastqc-before-2 {
-                pos:"-375 -705";
+                pos:"-360 -690";
                 style:simple;
                 bg-color-simple:"81 120 78 255";
                 in-file.angle:227.911;
             }
             get-pe-reads-list {
-                pos:"-600 -585";
+                pos:"-585 -570";
                 style:simple;
                 bg-color-simple:"23 106 239 255";
                 out.angle:1.50744;
             }
             kraken-classify {
-                pos:"-105 -435";
+                pos:"-165 -420";
+                style:simple;
+                bg-color-simple:"0 145 0 255";
+                in.angle:106.699;
+                out.angle:283.241;
+            }
+            metaphlan2-classify {
+                pos:"0 -420";
                 style:simple;
                 bg-color-simple:"0 145 0 255";
-                in.angle:90;
-                out.angle:244.179;
+                in.angle:126.529;
             }
             trimmomatic {
-                pos:"-330 -585";
+                pos:"-315 -570";
                 style:simple;
                 bg-color-simple:"127 127 127 255";
                 in.angle:180;
                 out.angle:360;
             }
             wevote-classify {
-                pos:"-375 -285";
+                pos:"-360 -270";
                 style:simple;
                 bg-color-simple:"0 106 0 255";
                 in.angle:349.046;
@@ -192,6 +206,9 @@ workflow "Parallel classification for PE reads"{
             trimmomatic.out->kraken-classify.in {
                 text-pos:"-3 7";
             }
+            trimmomatic.out->metaphlan2-classify.in {
+                text-pos:"-45 -43";
+            }
             wevote-classify.out->classification-report.in {
                 text-pos:"-48 4";
             }
@@ -300,6 +317,34 @@ workflow "Parallel classification for PE reads"{
             page {
                 id:5;
                 next:6;
+                title:"MetaPhlAn2 settings"
+                parameters-area {
+                    group {
+                        title:Classification;
+                        label-size:180;
+                        metaphlan2-classify.database {
+                        }
+                        metaphlan2-classify.analysis-type {
+                        }
+                        metaphlan2-classify.tax-level {
+                        }
+                        metaphlan2-classify.normalize-by-size {
+                        }
+                        metaphlan2-classify.presence-threshold {
+                        }
+                    }
+                    group {
+                        title:"Memory usage and efficiency";
+                        label-size:180;
+                        type:hideable;
+                        metaphlan2-classify.threads {
+                        }
+                    }
+                }
+            }
+            page {
+                id:6;
+                next:7;
                 title:"WEVOTE settings";
                 parameters-area {
                     group {
@@ -322,7 +367,7 @@ workflow "Parallel classification for PE reads"{
                 }
             }
             page {
-                id:6;
+                id:7;
                 title:"Output data";
                 parameters-area {
                     group {
@@ -334,6 +379,9 @@ workflow "Parallel classification for PE reads"{
                         clark-classify.output-url {
                             label:"CLARK output file";
                         }
+                        metaphlan2-classify.output-url {
+                            label:"MetaPhlAn2 output file"
+                        }
                         wevote-classify.output-url {
                             label:"WEVOTE output file";
                         }

data/workflow_samples/NGS/ngs_classification/ngs_classification_parallel/ngs_classification_parallel_single.uwl

@@ -48,12 +48,16 @@ workflow "Parallel classification for SE reads"{
         type:trimmomatic;
         name:Trimmomatic;
     }
+    metaphlan2-classify {
+        type:metaphlan2-classify;
+        name:MetaPhlAn2;
+    }
 
     .actor-bindings {
-        clark-classify.out->ensemble-classification.tax-data2
-        kraken-classify.out->ensemble-classification.tax-data1
         get-se-reads-list.out->fastqc-before.in-file
         get-se-reads-list.out->trimmomatic.in
+        kraken-classify.out->ensemble-classification.tax-data1
+        clark-classify.out->ensemble-classification.tax-data2
         diamond-classify.out->ensemble-classification.tax-data3
         ensemble-classification.out->wevote-classify.in
         wevote-classify.out->classification-report.in
@@ -61,6 +65,7 @@ workflow "Parallel classification for SE reads"{
         trimmomatic.out->diamond-classify.in
         trimmomatic.out->clark-classify.in
         trimmomatic.out->kraken-classify.in
+        trimmomatic.out->metaphlan2-classify.in
     }
 
     get-se-reads-list.reads-url1->fastqc-before.in-file.url
@@ -74,31 +79,32 @@ workflow "Parallel classification for SE reads"{
     ensemble-classification.url->wevote-classify.in.url
     wevote-classify.tax-data->classification-report.in.tax-data
     get-se-reads-list.reads-url1->trimmomatic.in.reads-url1
+    trimmomatic.reads-url1->metaphlan2-classify.in.reads-url1
 
     .meta {
         visual {
             clark-classify {
-                pos:"-360 -405";
+                pos:"-345 -390";
                 style:simple;
                 bg-color-simple:"0 145 0 255";
                 in.angle:95.5275;
                 out.angle:272.862;
             }
             classification-report {
-                pos:"45 -225";
+                pos:"45 -210";
                 style:simple;
                 bg-color-simple:"141 126 194 255";
                 in.angle:180;
             }
             diamond-classify {
-                pos:"-495 -405";
+                pos:"-480 -390";
                 style:simple;
                 bg-color-simple:"0 145 0 255";
                 in.angle:57.0948;
                 out.angle:288.925;
             }
             ensemble-classification {
-                pos:"-330 -225";
+                pos:"-315 -210";
                 style:simple;
                 bg-color-simple:"102 102 102 255";
                 out.angle:356.1;
@@ -107,39 +113,45 @@ workflow "Parallel classification for SE reads"{
                 tax-data3.angle:153.435;
             }
             fastqc-after {
-                pos:"-255 -705";
+                pos:"-240 -690";
                 style:simple;
                 bg-color-simple:"81 120 78 255";
                 in-file.angle:225;
             }
             fastqc-before {
-                pos:"-585 -705";
+                pos:"-570 -690";
                 style:simple;
                 bg-color-simple:"81 120 78 255";
                 in-file.angle:216.87;
             }
             get-se-reads-list {
-                pos:"-720 -600";
+                pos:"-705 -585";
                 style:simple;
                 bg-color-simple:"23 106 239 255";
                 out.angle:360;
             }
             kraken-classify {
-                pos:"-240 -405";
+                pos:"-225 -390";
                 style:simple;
                 bg-color-simple:"0 145 0 255";
                 in.angle:90;
                 out.angle:247.964;
             }
+            metaphlan2-classify {
+                pos:"-90 -390";
+                style:simple;
+                bg-color-simple:"0 145 0 255";
+                in.angle:144.638;
+            }
             trimmomatic {
-                pos:"-435 -600";
+                pos:"-420 -585";
                 style:simple;
                 bg-color-simple:"127 127 127 255";
                 in.angle:180;
                 out.angle:320.464;
             }
             wevote-classify {
-                pos:"-120 -225";
+                pos:"-105 -210";
                 style:simple;
                 bg-color-simple:"0 106 0 255";
                 in.angle:180;
@@ -173,7 +185,10 @@ workflow "Parallel classification for SE reads"{
                 text-pos:"-45 -43";
             }
             trimmomatic.out->kraken-classify.in {
-                text-pos:"20 2";
+                text-pos:"5 15";
+            }
+            trimmomatic.out->metaphlan2-classify.in {
+                text-pos:"67 9";
             }
             wevote-classify.out->classification-report.in {
                 text-pos:"-45 -43";
@@ -318,6 +333,34 @@ workflow "Parallel classification for SE reads"{
             page {
                 id:6;
                 next:7;
+                title:"MetaPhlAn2 settings"
+                parameters-area {
+                    group {
+                        title:Classification;
+                        label-size:180;
+                        metaphlan2-classify.database {
+                        }
+                        metaphlan2-classify.analysis-type {
+                        }
+                        metaphlan2-classify.tax-level {
+                        }
+                        metaphlan2-classify.normalize-by-size {
+                        }
+                        metaphlan2-classify.presence-threshold {
+                        }
+                    }
+                    group {
+                        title:"Memory usage and efficiency";
+                        label-size:180;
+                        type:hideable;
+                        metaphlan2-classify.threads {
+                        }
+                    }
+                }
+            }
+            page {
+                id:7;
+                next:8;
                 title:"WEVOTE settings";
                 parameters-area {
                     group {
@@ -340,7 +383,7 @@ workflow "Parallel classification for SE reads"{
                 }
             }
             page {
-                id:7;
+                id:8;
                 title:"Output data";
                 parameters-area {
                     group {
@@ -355,6 +398,9 @@ workflow "Parallel classification for SE reads"{
                         diamond-classify.output-url {
                             label:"DIAMOND output file";
                         }
+                        metaphlan2-classify.output-url {
+                            label:"MetaPhlAn2 output file"
+                        }
                         wevote-classify.output-url {
                             label:"WEVOTE output file";
                         }

data/workflow_samples/NGS/ngs_classification_parallel.uwl

@@ -6,9 +6,10 @@
 #   - Classify the pre-processed reads with Kraken.
 #   - Classify these reads with CLARK.
 #   - Classify these reads with DIAMOND (in case of SE reads).
-#   - Ensemble the classification output into a CSV file.
-#   - Improve classification with WEVOTE.
-#   - Provide general classification reports
+#   - Classify these reads with MetaPhlAn2.
+#   - Ensemble the classification output from Kraken, CLARK, and DIAMOND into a CSV file.
+#   - Improve classification from these tools with WEVOTE.
+#   - Provide general classification reports.
 
 workflow "Parallel NGS reads classification" {
     .meta {

debian/changelog

+ugene (33.0+dfsg-1) unstable; urgency=medium
+
+  * New upstream version.
+  * Standards-Version: 4.3.0 (no changes required)
+  * Adjusted patches
+    - Upstream now builds against regular sqlite almost by default
+    - UGENE_USE_BUNDLED_ZLIB=0 has remaining problems - changed default
+      to system sqlite by a patch
+    - Adjusted paths for dh_shlibdeps
+  * TODO: The package builds nicely but should experience some additional love
+          and testing. To mind come:
+    - reduce size of binaries by link-time optimization
+    - be nice and reduce the one or other compile time warning, some of which
+      are apparently in the Qt code?!?
+    - add runtime tests
+    - add a Debian Wiki page for the package
+
+ -- Steffen Moeller <moeller@debian.org>  Sat, 14 Dec 2019 12:56:14 +0100
+
 ugene (1.31.1+dfsg1-1) UNRELEASED; urgency=medium
 
   * Use UGENE_USE_BUNDLED_ZLIB=0

debian/control

@@ -7,9 +7,11 @@ Section: science
 Priority: optional
 Build-Depends: qtbase5-dev,
                libqt5webkit5-dev,
+               libqt5websockets5-dev,
                libqt5opengl5-dev,
                libqt5svg5-dev,
                qtscript5-dev,
+               qtwebengine5-dev,
                qt5-qmake,
                qtchooser,
                qttools5-dev,
@@ -20,7 +22,7 @@ Build-Depends: qtbase5-dev,
                libprocps-dev
 Build-Conflicts: libqt4-dev,
                  qt4-qmake
-Standards-Version: 4.3.0
+Standards-Version: 4.4.1
 Vcs-Browser: https://salsa.debian.org/med-team/ugene
 Vcs-Git: https://salsa.debian.org/med-team/ugene.git
 Homepage: http://ugene.unipro.ru

debian/copyright

@@ -189,6 +189,41 @@ License: BSD-2-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/libs_3rdparty/breakpad/src/common/convert_UTF.c src/libs_3rdparty/breakpad/src/common/convert_UTF.h
+Copyright: 1991-2015 Unicode, Inc.
+License: Unicode
+ Permission is hereby granted, free of charge, to any person obtaining
+ a copy of the Unicode data files and any associated documentation
+ (the "Data Files") or Unicode software and any associated documentation
+ (the "Software") to deal in the Data Files or Software
+ without restriction, including without limitation the rights to use,
+ copy, modify, merge, publish, distribute, and/or sell copies of
+ the Data Files or Software, and to permit persons to whom the Data Files
+ or Software are furnished to do so, provided that
+ (a) this copyright and permission notice appear with all copies 
+ of the Data Files or Software,
+ (b) this copyright and permission notice appear in associated 
+ documentation, and
+ (c) there is clear notice in each modified Data File or in the Software
+ as well as in the documentation associated with the Data File(s) or
+  Software that the data or software has been modified.
+ .
+ THE DATA FILES AND SOFTWARE 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 OF THIRD PARTY RIGHTS.
+ IN NO EVENT SHALL THE COPYRIGHT HOLDER OR HOLDERS INCLUDED IN THIS
+ NOTICE BE LIABLE FOR ANY CLAIM, OR ANY SPECIAL 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 THE DATA FILES OR SOFTWARE.
+ .
+ Except as contained in this notice, the name of a copyright holder
+ shall not be used in advertising or otherwise to promote the sale,
+ use or other dealings in these Data Files or Software without prior
+ written authorization of the copyright holder.
+
 Files: debian/*
 Copyright: © 2008-2011 Ivan Efremov <iefremov@unipro.ru>
            © 2012-2017 Andreas Tille <tille@debian.org>

debian/patches/add_missing_header.patch

@@ -2,8 +2,10 @@ Author:  Andreas Tille <tille@debian.org>
 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
-+++ b/src/plugins/external_tool_support/src/trimmomatic/steps/SlidingWindowStep.cpp
+Index: ugene/src/plugins/external_tool_support/src/trimmomatic/steps/SlidingWindowStep.cpp
+===================================================================
+--- ugene.orig/src/plugins/external_tool_support/src/trimmomatic/steps/SlidingWindowStep.cpp
++++ ugene/src/plugins/external_tool_support/src/trimmomatic/steps/SlidingWindowStep.cpp
 @@ -20,6 +20,7 @@
   */
  
@@ -12,13 +14,3 @@ Description: Fix build issue by adding missing headers
  
  #include "trimmomatic/util/LineEditHighlighter.h"
  #include "SlidingWindowStep.h"
---- a/src/plugins/external_tool_support/src/trimmomatic/util/LengthSettingsWidget.cpp
-+++ b/src/plugins/external_tool_support/src/trimmomatic/util/LengthSettingsWidget.cpp
-@@ -20,6 +20,7 @@
-  */
- 
- #include <U2Core/U2SafePoints.h>
-+#include <QIntValidator>
- 
- #include "LengthSettingsWidget.h"
- #include "LineEditHighlighter.h"

debian/patches/hardening.patch

@@ -8,22 +8,24 @@ Description: add QMAKE flags to add hardening
 Last-Updated: 2015-12-10
 Forwarded: no
 
---- a/src/ugene_globals.pri
-+++ b/src/ugene_globals.pri
-@@ -17,6 +17,11 @@ win32 : QMAKE_CXXFLAGS += /MP # use para
- win32 : DEFINES+= _WINDOWS
- win32-msvc2013 : DEFINES += _SCL_SECURE_NO_WARNINGS
+Index: ugene/src/ugene_globals.pri
+===================================================================
+--- ugene.orig/src/ugene_globals.pri
++++ ugene/src/ugene_globals.pri
+@@ -9,6 +9,11 @@ DEFINES+=UGENE_VER_MINOR=$${UGENE_VER_MI
+ 
+ CONFIG += c++11
  
 +CFLAGS   += $(CFLAGS)
 +CXXFLAGS += $(CXXFLAGS)
 +LDFLAGS  += $(LDFLAGS)
-+CPPFLAGS=$(CPPFLAGS)
++CPPFLAGS += $(CPPFLAGS)
 +
- win32 : QMAKE_CFLAGS_RELEASE = -O2 -Oy- -MD -Zi
- win32 : QMAKE_CXXFLAGS_RELEASE = -O2 -Oy- -MD -Zi
- win32 : QMAKE_LFLAGS_RELEASE = /INCREMENTAL:NO /MAP /MAPINFO:EXPORTS /DEBUG
-@@ -34,6 +39,10 @@ linux-g++ {
-     QMAKE_CXXFLAGS += -Wno-expansion-to-defined
+ # NGS package
+ _UGENE_NGS = $$(UGENE_NGS)
+ contains(_UGENE_NGS, 1) : DEFINES += UGENE_NGS
+@@ -55,6 +60,10 @@ linux-g++ {
+     }
  }
  
 +QMAKE_CXXFLAGS += $$(CXXFLAGS)

debian/patches/series

-use_debian_sqlite.patch
 hardening.patch
 add_missing_header.patch
 do_not_build_phylip.patch
 fix_desktop_file.patch
+# only partly addressed by upstream
+use_debian_sqlite.patch

debian/patches/use_debian_sqlite.patch

@@ -4,169 +4,10 @@ Description: Tried to use Debian packages sqlite3
  but failed because package does not build that way
 Forwarded: no
 Last-Updated: 2013-11-30
---- a/src/corelibs/U2Core/U2Core.pri
-+++ b/src/corelibs/U2Core/U2Core.pri
-@@ -20,7 +20,7 @@ use_bundled_zlib() {
- unix: QMAKE_CXXFLAGS += -Wno-char-subscripts
- 
- LIBS += -L../../_release
--LIBS += -lugenedb
-+LIBS += -lsqlite3
- 
- !debug_and_release|build_pass {
- 
-@@ -32,8 +32,6 @@ LIBS += -lugenedb
-             LIBS += -lzlibd
-             LIBS -= -lzlib
-         }
--        LIBS -= -lugenedb
--        LIBS += -lugenedbd
-     }
- 
-     CONFIG(release, debug|release) {
---- a/src/corelibs/U2Formats/U2Formats.pri
-+++ b/src/corelibs/U2Formats/U2Formats.pri
-@@ -14,7 +14,7 @@ UGENE_RELATIVE_DESTDIR = ''
- DEFINES += QT_FATAL_ASSERT BUILDING_U2FORMATS_DLL
- 
- LIBS += -L../../_release -lU2Core -lU2Algorithm
--LIBS += -lugenedb -lsamtools
-+LIBS += -lsqlite3 -lsamtools
- 
- win32-msvc2013 {
-     DEFINES += NOMINMAX _XKEYCHECK_H
-@@ -45,8 +45,8 @@ INCLUDEPATH += ../../libs_3rdparty/sqlit
- 
-     CONFIG(debug, debug|release) {
-         DESTDIR=../../_debug
--        LIBS -= -L../../_release -lU2Core -lU2Algorithm -lugenedb -lsamtools
--        LIBS += -L../../_debug -lU2Cored -lU2Algorithmd -lugenedbd -lsamtoolsd
-+        LIBS -= -L../../_release -lU2Core -lU2Algorithm -lsamtools
-+        LIBS += -L../../_debug -lU2Cored -lU2Algorithmd -lsamtoolsd
- 
-         win32-msvc2013 {
-             LIBS -= -lzlib
---- a/src/plugins/dbi_bam/dbi_bam.pri
-+++ b/src/plugins/dbi_bam/dbi_bam.pri
-@@ -12,7 +12,7 @@ use_bundled_zlib() {
-     macx: LIBS += -lz
- }
- 
--LIBS += -lugenedb -lsamtools
-+LIBS += -lsqlite3 -lsamtools
- 
- win32-msvc2013 {
-     DEFINES += NOMINMAX _XKEYCHECK_H
-@@ -37,8 +37,8 @@ win32 {
- !debug_and_release|build_pass {
- 
-     CONFIG(debug, debug|release) {
--        LIBS -= -lugenedb -lsamtools
--        LIBS += -lugenedbd -lsamtoolsd
-+        LIBS -= -lsamtools
-+        LIBS += -lsamtoolsd
- 
-         win32-msvc2013 {
-             LIBS -= -lzlib
---- a/src/corelibs/U2Script/U2Script.pri
-+++ b/src/corelibs/U2Script/U2Script.pri
-@@ -21,15 +21,15 @@ INCLUDEPATH +=      ../../include \
- #                    $${UGENE_NODE_DIR}/deps/uv/include
- #}
- 
--LIBS += -L../../_release -lU2Core -lU2Algorithm -lU2Formats -lU2Lang -lU2Private -lugenedb -lU2Gui -lU2Test
-+LIBS += -L../../_release -lU2Core -lU2Algorithm -lU2Formats -lU2Lang -lU2Private -lsqlite3 -lU2Gui -lU2Test
- 
- !debug_and_release|build_pass {
- 
-     CONFIG( debug, debug|release ) {
-         DESTDIR =   ../../_debug
- 
--        LIBS -=     -L../../_release -lU2Core -lU2Algorithm -lU2Formats -lU2Lang -lU2Private -lugenedb -lU2Gui -lU2Test
--        LIBS +=     -L../../_debug -lU2Cored -lU2Algorithmd -lU2Formatsd -lU2Langd -lU2Privated -lugenedbd -lU2Guid -lU2Testd
-+        LIBS -=     -L../../_release -lU2Core -lU2Algorithm -lU2Formats -lU2Lang -lU2Private -lsqlite3 -lU2Gui -lU2Test
-+        LIBS +=     -L../../_debug -lU2Cored -lU2Algorithmd -lU2Formatsd -lU2Langd -lU2Privated -lsqlite3 -lU2Guid -lU2Testd
-                     
- #        count( UGENE_NODE_DIR, 1 ) {
- #            LIBS += -l$${UGENE_NODE_DIR}/Debug/node
---- a/src/plugins_checker/plugins_checker.pri
-+++ b/src/plugins_checker/plugins_checker.pri
-@@ -15,7 +15,7 @@ CONFIG -= app_bundle
- DEFINES+= QT_DLL QT_FATAL_ASSERT
- INCLUDEPATH += src _tmp ../include ../corelibs/U2Private/src
- 
--LIBS += -L../_release -lU2Core -lU2Algorithm -lU2Formats -lU2Gui -lU2Private -lugenedb -lbreakpad
-+LIBS += -L../_release -lU2Core -lU2Algorithm -lU2Formats -lU2Gui -lU2Private -lsqlite3 -lbreakpad
- 
- !debug_and_release|build_pass {
- 
-@@ -25,8 +25,8 @@ LIBS += -L../_release -lU2Core -lU2Algor
-         DESTDIR=../_debug
-         MOC_DIR=_tmp/moc/debug
-         OBJECTS_DIR=_tmp/obj/debug
--        LIBS -= -L../_release -lU2Core -lU2Algorithm -lU2Formats -lU2Gui -lU2Private -lugenedb -lbreakpad
--        LIBS += -L../_debug -lU2Cored -lU2Algorithmd -lU2Formatsd -lU2Guid -lU2Privated -lugenedbd -lbreakpadd
-+        LIBS -= -L../_release -lU2Core -lU2Algorithm -lU2Formats -lU2Gui -lU2Private -lsqlite3 -lbreakpad
-+        LIBS += -L../_debug -lU2Cored -lU2Algorithmd -lU2Formatsd -lU2Guid -lU2Privated -lsqlite3 -lbreakpadd
-     }
- 
-     CONFIG(release, debug|release) {
---- a/ugene.pro
-+++ b/ugene.pro
-@@ -22,7 +22,6 @@ use_bundled_zlib() {
- SUBDIRS += \
-           src/libs_3rdparty/breakpad \
-           src/libs_3rdparty/qscore \
--          src/libs_3rdparty/sqlite3 \
-           src/libs_3rdparty/samtools \
-           src/libs_3rdparty/QSpec \
-           src/corelibs/U2Core \
---- a/src/ugenecl/ugenecl.pri
-+++ b/src/ugenecl/ugenecl.pri
-@@ -14,7 +14,7 @@ CONFIG +=qt dll thread debug_and_release
- DEFINES+= QT_DLL QT_FATAL_ASSERT
- INCLUDEPATH += src _tmp ../include ../corelibs/U2Private/src
- 
--LIBS += -L../_release -lU2Core -lU2Algorithm -lU2Formats -lU2Gui -lU2Test -lU2Lang -lU2Private -lugenedb -lbreakpad -lQSpec
-+LIBS += -L../_release -lU2Core -lU2Algorithm -lU2Formats -lU2Gui -lU2Test -lU2Lang -lU2Private -lsqlite3 -lbreakpad -lQSpec
- if(exclude_list_enabled()|!exists( ../libs_3rdparty/QSpec/QSpec.pro )) {
-     LIBS -= -lQSpec
- }
-@@ -26,8 +26,8 @@ if(exclude_list_enabled()|!exists( ../li
-         DESTDIR=../_debug
-         MOC_DIR=_tmp/moc/debug
-         OBJECTS_DIR=_tmp/obj/debug
--        LIBS -= -L../_release -lU2Core -lU2Algorithm -lU2Formats -lU2Gui -lU2Test -lU2Lang -lU2Private -lugenedb -lbreakpad -lQSpec
--        LIBS += -L../_debug -lU2Cored -lU2Algorithmd -lU2Formatsd -lU2Guid -lU2Testd -lU2Langd -lU2Privated -lugenedbd -lbreakpadd -lQSpecd
-+        LIBS -= -L../_release -lU2Core -lU2Algorithm -lU2Formats -lU2Gui -lU2Test -lU2Lang -lU2Private -lbreakpad -lQSpec
-+        LIBS += -L../_debug -lU2Cored -lU2Algorithmd -lU2Formatsd -lU2Guid -lU2Testd -lU2Langd -lU2Privated -lbreakpadd -lQSpecd
-         if(exclude_list_enabled()|!exists( ../libs_3rdparty/QSpec/QSpec.pro )) {
-             LIBS -= -lQSpecd
-         }
---- a/src/ugeneui/ugeneui.pri
-+++ b/src/ugeneui/ugeneui.pri
-@@ -16,7 +16,7 @@ DEFINES+= QT_DLL QT_FATAL_ASSERT
- INCLUDEPATH += src _tmp ../include ../corelibs/U2Private/src ../libs_3rdparty/QSpec/src
- macx : INCLUDEPATH += /System/Library/Frameworks/Security.framework/Headers
- 
--LIBS += -L../_release -lU2Core -lU2Algorithm -lU2Formats -lU2Gui -lU2View -lU2Test -lU2Lang -lU2Private -lugenedb -lbreakpad -lQSpec
-+LIBS += -L../_release -lU2Core -lU2Algorithm -lU2Formats -lU2Gui -lU2View -lU2Test -lU2Lang -lU2Private -lsqlite3 -lbreakpad -lQSpec
- macx: LIBS += /System/Library/Frameworks/Security.framework/Security
- if(exclude_list_enabled()|!exists( ../libs_3rdparty/QSpec/QSpec.pro )) {
-     LIBS -= -lQSpec
-@@ -31,8 +31,8 @@ if(exclude_list_enabled()|!exists( ../li
-         DESTDIR=../_debug
-         MOC_DIR=_tmp/moc/debug
-         OBJECTS_DIR=_tmp/obj/debug
--        LIBS -= -L../_release -lU2Core -lU2Algorithm -lU2Formats -lU2Gui -lU2View -lU2Test -lU2Lang -lU2Private -lugenedb -lbreakpad -lQSpec
--        LIBS += -L../_debug -lU2Cored -lU2Algorithmd -lU2Formatsd -lU2Guid -lU2Viewd -lU2Testd -lU2Langd -lU2Privated -lugenedbd -lbreakpadd -lQSpecd
-+        LIBS -= -L../_release -lU2Core -lU2Algorithm -lU2Formats -lU2Gui -lU2View -lU2Test -lU2Lang -lU2Private -lbreakpad -lQSpec
-+        LIBS += -L../_debug -lU2Cored -lU2Algorithmd -lU2Formatsd -lU2Guid -lU2Viewd -lU2Testd -lU2Langd -lU2Privated -lbreakpadd -lQSpecd
-         if(exclude_list_enabled()|!exists( ../libs_3rdparty/QSpec/QSpec.pro )) {
-             LIBS -= -lQSpecd
-         }
---- a/src/corelibs/U2Core/src/dbi/U2SQLiteTripleStore.cpp
-+++ b/src/corelibs/U2Core/src/dbi/U2SQLiteTripleStore.cpp
+Index: ugene/src/corelibs/U2Core/src/dbi/U2SQLiteTripleStore.cpp
+===================================================================
+--- ugene.orig/src/corelibs/U2Core/src/dbi/U2SQLiteTripleStore.cpp
++++ ugene/src/corelibs/U2Core/src/dbi/U2SQLiteTripleStore.cpp
 @@ -19,7 +19,7 @@
   * MA 02110-1301, USA.
   */
@@ -176,14 +17,10 @@ Last-Updated: 2013-11-30
  
  #include <U2Core/Log.h>
  #include <U2Core/U2SafePoints.h>
---- a/src/include/3rdparty/sqlite3/sqlite3.h
-+++ b/src/include/3rdparty/sqlite3/sqlite3.h
-@@ -1 +1 @@
--#include "../../../libs_3rdparty/sqlite3/src/sqlite3.h"
-\ No newline at end of file
-+#include "sqlite3.h"
---- a/src/corelibs/U2Core/src/dbi/U2SqlHelpers.cpp
-+++ b/src/corelibs/U2Core/src/dbi/U2SqlHelpers.cpp
+Index: ugene/src/corelibs/U2Core/src/dbi/U2SqlHelpers.cpp
+===================================================================
+--- ugene.orig/src/corelibs/U2Core/src/dbi/U2SqlHelpers.cpp
++++ ugene/src/corelibs/U2Core/src/dbi/U2SqlHelpers.cpp
 @@ -25,7 +25,7 @@
  #include <U2Core/U2DbiUtils.h>
  #include <U2Core/U2SafePoints.h>
@@ -193,8 +30,10 @@ Last-Updated: 2013-11-30
  
  namespace U2 {
  
---- a/src/corelibs/U2Formats/src/sqlite_dbi/SQLiteBlobInputStream.cpp
-+++ b/src/corelibs/U2Formats/src/sqlite_dbi/SQLiteBlobInputStream.cpp
+Index: ugene/src/corelibs/U2Formats/src/sqlite_dbi/SQLiteBlobInputStream.cpp
+===================================================================
+--- ugene.orig/src/corelibs/U2Formats/src/sqlite_dbi/SQLiteBlobInputStream.cpp
++++ ugene/src/corelibs/U2Formats/src/sqlite_dbi/SQLiteBlobInputStream.cpp
 @@ -19,7 +19,7 @@
   * MA 02110-1301, USA.
   */
@@ -204,8 +43,10 @@ Last-Updated: 2013-11-30
  
  #include <U2Core/U2DbiUtils.h>
  #include <U2Core/U2SafePoints.h>
---- a/src/corelibs/U2Formats/src/sqlite_dbi/SQLiteBlobOutputStream.cpp
-+++ b/src/corelibs/U2Formats/src/sqlite_dbi/SQLiteBlobOutputStream.cpp
+Index: ugene/src/corelibs/U2Formats/src/sqlite_dbi/SQLiteBlobOutputStream.cpp
+===================================================================
+--- ugene.orig/src/corelibs/U2Formats/src/sqlite_dbi/SQLiteBlobOutputStream.cpp
++++ ugene/src/corelibs/U2Formats/src/sqlite_dbi/SQLiteBlobOutputStream.cpp
 @@ -19,7 +19,7 @@
   * MA 02110-1301, USA.
   */
@@ -215,8 +56,10 @@ Last-Updated: 2013-11-30
  
  #include <U2Core/U2SafePoints.h>
  #include <U2Core/UdrSchema.h>
---- a/src/corelibs/U2Formats/src/sqlite_dbi/SQLiteDbi.cpp
-+++ b/src/corelibs/U2Formats/src/sqlite_dbi/SQLiteDbi.cpp
+Index: ugene/src/corelibs/U2Formats/src/sqlite_dbi/SQLiteDbi.cpp
+===================================================================
+--- ugene.orig/src/corelibs/U2Formats/src/sqlite_dbi/SQLiteDbi.cpp
++++ ugene/src/corelibs/U2Formats/src/sqlite_dbi/SQLiteDbi.cpp
 @@ -41,7 +41,7 @@
  
  #include <QFile>
@@ -226,8 +69,10 @@ Last-Updated: 2013-11-30
  
  namespace U2 {
  
---- a/src/plugins/dbi_bam/src/Dbi.cpp
-+++ b/src/plugins/dbi_bam/src/Dbi.cpp
+Index: ugene/src/plugins/dbi_bam/src/Dbi.cpp
+===================================================================
+--- ugene.orig/src/plugins/dbi_bam/src/Dbi.cpp
++++ ugene/src/plugins/dbi_bam/src/Dbi.cpp
 @@ -33,7 +33,7 @@
  #include <U2Core/U2OpStatusUtils.h>
  #include <U2Core/IOAdapterUtils.h>
@@ -237,3 +82,18 @@ Last-Updated: 2013-11-30
  
  namespace U2 {
  namespace BAM {
+Index: ugene/src/ugene_globals.pri
+===================================================================
+--- ugene.orig/src/ugene_globals.pri
++++ ugene/src/ugene_globals.pri
+@@ -197,8 +197,8 @@ defineReplace(add_z_lib) {
+ # To use locally installed sqlite library use UGENE_USE_BUNDLED_SQLITE = 0
+ 
+ defineTest( use_bundled_sqlite ) {
+-    contains( UGENE_USE_BUNDLED_SQLITE, 0 ) : return (false)
+-    return (true)
++    contains( UGENE_USE_BUNDLED_SQLITE, 1 ) : return (true)
++    return (false)
+ }
+ 
+ use_bundled_sqlite() {

debian/rules

@@ -13,7 +13,8 @@ export DEB_BUILD_MAINT_OPTIONS = hardening=+all
 
 override_dh_auto_configure:
 	# exclude non-free plugins
-	dh_auto_configure -- QMAKE_CFLAGS_ISYSTEM= QMAKE_CXXFLAGS_ISYSTEM= UGENE_WITHOUT_NON_FREE=1 UGENE_LRELEASE=lrelease-qt5 UGENE_LUPDATE=lupdate-qt5 UGENE_USE_BUNDLED_ZLIB=0
+	dh_auto_configure -- QMAKE_CFLAGS_ISYSTEM= QMAKE_CXXFLAGS_ISYSTEM= UGENE_WITHOUT_NON_FREE=1 UGENE_LRELEASE=lrelease-qt5 UGENE_LUPDATE=lupdate-qt5
+	#UGENE_USE_BUNDLED_ZLIB=0
 
 	find . -name Makefile.* | xargs -r sed -i '/STRIP/d'
 
@@ -23,6 +24,8 @@ override_dh_auto_configure:
 override_dh_auto_clean:
 	dh_auto_clean
 	rm -rf src/_debug src/_release ugene
+	rm -f .qmake.stash
+	rm -f src/libs_3rdparty/sqlite3/Makefile src/libs_3rdparty/sqlite3/Makefile.Debug src/libs_3rdparty/sqlite3/Makefile.Release
 
 override_dh_auto_install:
 	dh_auto_install
@@ -38,7 +41,7 @@ override_dh_fixperms-indep:
 	rm -f debian/ugene-data/usr/share/ugene/data/license
 
 override_dh_shlibdeps:
-	dh_shlibdeps -l$(CURDIR)/debian/$(DEB_SOURCE)/usr/lib/$(DEB_SOURCE)/:/build/ugene-1.31.1+dfsg/debian/$(DEB_SOURCE)/usr/lib/$(DEB_SOURCE)/plugins/
+	dh_shlibdeps -l$(CURDIR)/debian/tmp/usr/lib/ugene/plugins/:$(CURDIR)/debian/tmp/usr/lib/ugene:$(CURDIR)/debian/$(DEB_SOURCE)/usr/lib/$(DEB_SOURCE)/
 
 override_dh_dwz:
 	echo "Do not run dh_dwz since it just results in:"

debian/source/lintian-overrides

+# The license in the file explicitly states that the file can be modified
+ugene source: license-problem-convert-utf-code src/libs_3rdparty/breakpad/src/common/convert_UTF.c

installer/_common_data/ugene

@@ -26,10 +26,10 @@ dirname=$(dirname "`readlink -f "$0"`")
 tmp="${dirname#?}"
 
 if [ "${dirname%$tmp}" != "/" ]; then
-    dirname=$PWD/$dirname
+    dirname="$PWD/$dirname"
 fi
 
-LD_LIBRARY_PATH=$dirname
+LD_LIBRARY_PATH="$dirname"
 export LD_LIBRARY_PATH
 
 # check compatibility OS and UGENE (32-bit or 64-bit)
@@ -44,7 +44,7 @@ esac
 ugene_i686=false
 ugene_x86_64=false
 
-case "`file -b $dirname/$appname |cut -d "," -f1 |grep 64|wc -l|tr -d ' '`" in
+case "`file -b \"$dirname\"/\"$appname\" |cut -d "," -f1 |grep 64|wc -l|tr -d ' '`" in
 0*) ugene_i686=true;;
 1*) ugene_x86_64=true;;
 esac
@@ -63,8 +63,8 @@ fi
 export QT_QPA_PLATFORMTHEME=
 
 if [ -z $IS_KDE ]; then
-    "$dirname/$appname" "${params[@]}"
+    "$dirname"/"$appname" "${params[@]}"
 else
-    "$dirname/$appname" "${params[@]}" -style cleanlooks
+    "$dirname"/"$appname" "${params[@]}" -style cleanlooks
 fi
 

installer/linux/X11/create_bundle.sh

 # this script's home dir is trunk/installer/linux/X11
 
 PRODUCT_NAME="ugene"
-VERSION=`cat ../../../src/ugene_version.pri | grep UGENE_VERSION | awk -F'=' '{print $2}'`
+
+VERSION_MAJOR=`cat ../../../src/ugene_version.pri | grep 'UGENE_VER_MAJOR=' | awk -F'=' '{print $2}'`
+VERSION_MINOR=`cat ../../../src/ugene_version.pri | grep 'UGENE_VER_MINOR=' | awk -F'=' '{print $2}'`
+VERSION=`cat ../../../src/ugene_version.pri | grep UGENE_VERSION | awk -F'=' '{print $2}' | \
+         sed -e 's/$${UGENE_VER_MAJOR}/'"$VERSION_MAJOR"'/g' \
+             -e 's/$${UGENE_VER_MINOR}/'"$VERSION_MINOR"'/g'`
+
 RELEASE_DIR=../../../src/_release
 SYMBOLS_DIR=symbols
 DUMP_SYMBOLS_LOG=dump_symbols_log.txt
@@ -190,6 +196,7 @@ add-plugin hmm2
 add-plugin kalign
 add-plugin kraken_support
 add-plugin linkdata_support
+add-plugin metaphlan2_support
 add-plugin ngs_reads_classification
 add-plugin orf_marker
 add-plugin opencl_support