Update to 1.31.0

PR:		229463
Approved by:	Hannes Hauswedell <h2+fbsdports@fsfe.org> (maintainer)

17 files changed, 201 insertions, 181 deletions

diff --git a/biology/ugene/Makefile b/biology/ugene/Makefile
index 66460d5de368..244b3a8c8754 100644
--- a/biology/ugene/Makefile
+++ b/biology/ugene/Makefile
@@ -2,8 +2,7 @@
 # $FreeBSD$
 
 PORTNAME=	ugene
-DISTVERSION=	1.22.0
-PORTREVISION=	3
+DISTVERSION=	1.31.0
 CATEGORIES=	biology science
 MASTER_SITES=	http://ugene.unipro.ru/downloads/
 DISTFILES=	${DISTNAME}${EXTRACT_SUFX} QueryDesigner_UserManual.pdf \
@@ -14,46 +13,42 @@ EXTRACT_ONLY=	${DISTNAME}${EXTRACT_SUFX}
 MAINTAINER=	h2+fbsdports@fsfe.org
 COMMENT=	Free, open-source, cross-platform bioinformatics toolkit
 
-LICENSE=	GPLv2
+LICENSE=	GPLv2+
+LICENSE_FILE=	${WRKSRC}/LICENSE.txt
 
 RUN_DEPENDS=	bash:shells/bash
 
 BROKEN_aarch64=	Fails to build: invokes x86 asm
 
-USES=		desktop-file-utils qmake qt:5
-USE_GL=		glu
-USE_QT=		buildtools_build linguisttools_build scripttools_build \
-		gui network printsupport script sql svg webkit widgets xml \
+USES=		desktop-file-utils qmake qt:5 shared-mime-info
+USE_GL=		gl glu
+USE_QT=		buildtools_build linguisttools_build \
+		core gui network opengl printsupport script scripttools \
+		sql svg testlib webkit widgets xml \
 		imageformats_run
+USE_XORG=	x11 xtst
 
 QMAKE_ARGS=	INSTALL_PREFIX="${PREFIX}" UGENE_INSTALL_DATA="${DATADIR}" \
 		INSTALL_MANDIR="${MAN1PREFIX}/man" LRELEASE="${LRELEASE}" \
 		LUPDATE="${LUPDATE}"
 ALL_TARGET=	release
 
-# Required for Google Test code
-CXXFLAGS+=	-std=c++11
-
 DOCSDIR=	${DATADIR}/manuals
 
-OPTIONS_DEFINE=	DOCS
+OPTIONS_DEFINE=	DOCS OPENCL
 DOCS_DESC=	Install official UGENE documentation (PDF)
 
+OPENCL_QMAKE_ON=	UGENE_OPENCL_DETECTED=1
+
 .include <bsd.port.pre.mk>
 
 .if ${ARCH} == amd64
 # XXX: need to manually tell the build we are on x64
 QMAKE_ARGS+=	CONFIG+=x64
-PLIST_SUB+=	NOX64="@comment "
-.else
-PLIST_SUB+=	NOX64=""
 .endif
 
 .if ${MACHINE_CPU:Msse2}
 QMAKE_ARGS+=	UGENE_SSE2_DETECTED=1
-PLIST_SUB+=	SSE2=""
-.else
-PLIST_SUB+=	SSE2="@comment "
 .endif
 
 post-extract:
@@ -67,8 +62,6 @@ post-patch:
 		${WRKSRC}/installer/_common_data/ugene
 	@${REINPLACE_CMD} -e 's|-bit version|& for ${OPSYS}/${ARCH}|' \
 		${WRKSRC}/src/ugeneui/src/main_window/AboutDialogController.cpp
-	@${REINPLACE_CMD} -e '/unix_not_mac/,+11d' \
-		${WRKSRC}/src/corelibs/U2Core/U2Core.pri
 	@${REINPLACE_CMD} 's, -lbreakpad,,' \
 		${WRKSRC}/src/corelibs/U2Private/U2Private.pri \
 		${WRKSRC}/src/plugins_checker/plugins_checker.pri \
diff --git a/biology/ugene/distinfo b/biology/ugene/distinfo
index 7d22d9d84ea9..d85231b953aa 100644
--- a/biology/ugene/distinfo
+++ b/biology/ugene/distinfo
@@ -1,5 +1,6 @@
-SHA256 (ugene/ugene-1.22.0.tar.gz) = ee46be799c9f02a9b6a89f13747a4918d5c96c01676dc2d4cc4a4c98278912b6
-SIZE (ugene/ugene-1.22.0.tar.gz) = 20986853
+TIMESTAMP = 1535840965
+SHA256 (ugene/ugene-1.31.0.tar.gz) = d1f46306834a292618cc54b31060b69da5b0b18da311a55bf82ab42f5a434320
+SIZE (ugene/ugene-1.31.0.tar.gz) = 20656562
 SHA256 (ugene/QueryDesigner_UserManual.pdf) = 5d232c0de7e9d1fd32b8ee0a78f9f4abe1ab9d6536ec3958c47de29f3096faf4
 SIZE (ugene/QueryDesigner_UserManual.pdf) = 855662
 SHA256 (ugene/UniproUGENE_UserManual.pdf) = ae6aef32a6e92a30ba7c36cdd894a8caf634d678f15da7ad9eab52b6f40b9ed6
diff --git a/biology/ugene/files/patch-git_279756e4 b/biology/ugene/files/patch-git_279756e4
deleted file mode 100644
index f730ce8fe3c4..000000000000
--- a/biology/ugene/files/patch-git_279756e4
+++ /dev/null
@@ -1,30 +0,0 @@
-From 279756e448f53af5a495a2ce3a12abdf833fc703 Mon Sep 17 00:00:00 2001
-From: Kevin Kofler <kevin.kofler@chello.at>
-Date: Tue, 2 Jan 2018 22:21:03 +0100
-Subject: [PATCH] Fix build against Qt 5.10
-MIME-Version: 1.0
-Content-Type: text/plain; charset=UTF-8
-Content-Transfer-Encoding: 8bit
-
-src/plugins/external_tool_support/src/bowtie2/Bowtie2Settings.ui: Remove
-shortcut setting that breaks the build with Qt 5.10.
-
-UGENE can be built with Qt ≥ 5.6 and a separate QtWebKit. With Qt 5.10,
-we were hitting a build error: uic was producing code that did not
-compile.
----
- src/plugins/external_tool_support/src/bowtie2/Bowtie2Settings.ui | 3 ---
- 1 file changed, 3 deletions(-)
-
---- src/plugins/external_tool_support/src/ui/Bowtie2Settings.ui
-+++ src/plugins/external_tool_support/src/ui/Bowtie2Settings.ui
-@@ -254,9 +254,6 @@
-             <property name="text">
-              <string>Disallow gaps (--gbar)</string>
-             </property>
--            <property name="shortcut">
--             <string notr="true"/>
--            </property>
-            </widget>
-           </item>
-          </layout>
diff --git a/biology/ugene/files/patch-git_578c949 b/biology/ugene/files/patch-git_578c949
new file mode 100644
index 000000000000..8b11562770d1
--- /dev/null
+++ b/biology/ugene/files/patch-git_578c949
@@ -0,0 +1,25 @@
+From 578c949ae7df017e23c3eda0293faa3db718c89f Mon Sep 17 00:00:00 2001
+From: Yuliya Algaer <yalgaer@gmail.com>
+Date: Fri, 24 Aug 2018 21:24:12 +0700
+Subject: [PATCH] Build fix for Fedora
+
+--- src/plugins/external_tool_support/src/trimmomatic/util/LengthSettingsWidget.cpp.orig	2018-08-16 13:58:58 UTC
++++ 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"
+--- src/plugins/external_tool_support/src/trimmomatic/util/QualitySettingsWidget.cpp.orig	2018-08-16 13:58:58 UTC
++++ src/plugins/external_tool_support/src/trimmomatic/util/QualitySettingsWidget.cpp
+@@ -19,6 +19,7 @@
+  * MA 02110-1301, USA.
+  */
+ 
++#include <QIntValidator>
+ #include <U2Core/U2SafePoints.h>
+ 
+ #include "QualitySettingsWidget.h"
diff --git a/biology/ugene/files/patch-src_corelibs_U2Private_U2Private.pro b/biology/ugene/files/patch-src_corelibs_U2Private_U2Private.pro
index e75866cbf3c6..73f2d4038887 100644
--- a/biology/ugene/files/patch-src_corelibs_U2Private_U2Private.pro
+++ b/biology/ugene/files/patch-src_corelibs_U2Private_U2Private.pro
@@ -1,4 +1,4 @@
---- src/corelibs/U2Private/U2Private.pro.orig	2016-03-31 12:22:14 UTC
+--- src/corelibs/U2Private/U2Private.pro.orig	2018-08-16 13:59:12 UTC
 +++ src/corelibs/U2Private/U2Private.pro
 @@ -12,12 +12,7 @@ HEADERS += src/AppContextImpl.h \
             src/PluginSupportImpl.h \
@@ -14,7 +14,7 @@
  
  SOURCES += src/AppContextImpl.cpp \
             src/AppSettingsImpl.cpp \
-@@ -30,29 +25,7 @@ SOURCES += src/AppContextImpl.cpp \
+@@ -30,23 +25,13 @@ SOURCES += src/AppContextImpl.cpp \
             src/PluginSupportImpl.cpp \
             src/ServiceRegistryImpl.cpp \
             src/SettingsImpl.cpp \
@@ -26,22 +26,16 @@
 -           src/crash_handler/StackWalker.cpp
 +           src/TaskSchedulerImpl.cpp
  
- TRANSLATIONS += transl/english.ts \
-                 transl/russian.ts
--
--win32 {
--    HEADERS += src/crash_handler/CrashHandlerPrivateWin.h
--    SOURCES += src/crash_handler/CrashHandlerPrivateWin.cpp
+ TRANSLATIONS += transl/russian.ts
+ 
+ win32 {
+     HEADERS += src/crash_handler/CrashHandlerPrivateWin.h
+     SOURCES += src/crash_handler/CrashHandlerPrivateWin.cpp
 -}
 -
 -unix_not_mac() {
 -    HEADERS += src/crash_handler/CrashHandlerPrivateUnixNotMac.h
 -    SOURCES += src/crash_handler/CrashHandlerPrivateUnixNotMac.cpp
--}
--
--mac {
--    HEADERS += src/crash_handler/CrashHandlerPrivateMac.h \
--               src/SleepPreventerMac.h
--    SOURCES += src/crash_handler/CrashHandlerPrivateMac.cpp \
--               src/SleepPreventerMac.cpp
--}
+ }
+ 
+ mac {
diff --git a/biology/ugene/files/patch-src_libs__3rdparty_QSpec_src_drivers_GTKeyboardDriverLinux.cpp b/biology/ugene/files/patch-src_libs__3rdparty_QSpec_src_drivers_GTKeyboardDriverLinux.cpp
new file mode 100644
index 000000000000..cc2164cb1db0
--- /dev/null
+++ b/biology/ugene/files/patch-src_libs__3rdparty_QSpec_src_drivers_GTKeyboardDriverLinux.cpp
@@ -0,0 +1,22 @@
+Use the Linux driver for FreeBSD as well. Fixes crash on startup.
+
+--- src/libs_3rdparty/QSpec/src/drivers/GTKeyboardDriverLinux.cpp.orig	2018-09-02 00:22:54 UTC
++++ src/libs_3rdparty/QSpec/src/drivers/GTKeyboardDriverLinux.cpp
+@@ -22,7 +22,7 @@
+ #include <cctype>
+ #include "GTKeyboardDriver.h"
+ 
+-#if defined __linux__
++#if defined(__linux__) || defined(__FreeBSD__)
+     #define XK_LATIN1      // for latin symbol
+     #define XK_MISCELLANY  // for action keys
+     #include <X11/keysymdef.h>
+@@ -31,7 +31,7 @@
+ 
+ namespace HI {
+ 
+-#if defined __linux__
++#if defined(__linux__) || defined(__FreeBSD__)
+ 
+ #define GT_CLASS_NAME "GTKeyboardDriverLinux"
+ 
diff --git a/biology/ugene/files/patch-src_libs__3rdparty_QSpec_src_drivers_GTMouseDriverLinux.cpp b/biology/ugene/files/patch-src_libs__3rdparty_QSpec_src_drivers_GTMouseDriverLinux.cpp
new file mode 100644
index 000000000000..8dfdd9b7d53f
--- /dev/null
+++ b/biology/ugene/files/patch-src_libs__3rdparty_QSpec_src_drivers_GTMouseDriverLinux.cpp
@@ -0,0 +1,20 @@
+Use the Linux driver for FreeBSD as well. Fixes crash on startup.
+
+--- src/libs_3rdparty/QSpec/src/drivers/GTMouseDriverLinux.cpp.orig	2018-09-02 00:23:24 UTC
++++ src/libs_3rdparty/QSpec/src/drivers/GTMouseDriverLinux.cpp
+@@ -22,13 +22,13 @@
+ #include "GTMouseDriver.h"
+ #include <QByteArray>
+ 
+-#ifdef __linux__
++#if defined(__linux__) || defined(__FreeBSD__)
+     #include <X11/extensions/XTest.h>
+ #endif
+ 
+ namespace HI {
+ 
+-#ifdef __linux__
++#if defined(__linux__) || defined(__FreeBSD__)
+ 
+ #define GT_CLASS_NAME "GTMouseDriver Linux"
+ QPoint GTMouseDriver::mousePos = QPoint(-1, -1);
diff --git a/biology/ugene/files/patch-src_libs__3rdparty_samtools_samtools.pri b/biology/ugene/files/patch-src_libs__3rdparty_samtools_samtools.pri
deleted file mode 100644
index 3951d5f87ecb..000000000000
--- a/biology/ugene/files/patch-src_libs__3rdparty_samtools_samtools.pri
+++ /dev/null
@@ -1,11 +0,0 @@
---- src/libs_3rdparty/samtools/samtools.pri.orig	2016-03-31 12:21:56 UTC
-+++ src/libs_3rdparty/samtools/samtools.pri
-@@ -3,7 +3,7 @@ UGENE_RELATIVE_DESTDIR = ''
- 
- TEMPLATE = lib
- CONFIG +=thread debug_and_release staticlib warn_off
--INCLUDEPATH += src src/samtools ../../include /usr/include
-+INCLUDEPATH += src src/samtools ../../include
- win32 : INCLUDEPATH += src/samtools/win32
- DEFINES+="_FILE_OFFSET_BITS=64" _LARGEFILE64_SOURCE _USE_KNETFILE
- win32 : DEFINES += _USE_MATH_DEFINES "inline=__inline" "__func__=__FUNCTION__" "R_OK=4" "atoll=_atoi64" "alloca=_alloca"
diff --git a/biology/ugene/files/patch-src_plugins__3rdparty_phylip_src_phylip.h b/biology/ugene/files/patch-src_plugins__3rdparty_phylip_src_phylip.h
deleted file mode 100644
index cf733a59a1de..000000000000
--- a/biology/ugene/files/patch-src_plugins__3rdparty_phylip_src_phylip.h
+++ /dev/null
@@ -1,10 +0,0 @@
---- src/plugins_3rdparty/phylip/src/phylip.h.orig	2017-12-30 19:54:56 UTC
-+++ src/plugins_3rdparty/phylip/src/phylip.h
-@@ -271,7 +271,6 @@ MALLOCRETURN    *mymalloc(long);
- #define MAXNCH          30   /* must be greater than or equal to nmlngth */
- #define maxcategs       9    /* maximum number of site types */
- #define maxcategs2     11    /* maximum number of site types + 2 */
--#define point           "."
- #define pointe          '.'
- #define down            2
- #define MAXSHIMOTREES 100
diff --git a/biology/ugene/files/patch-src_plugins__3rdparty_umuscle_src_MuscleWorkPool.cpp b/biology/ugene/files/patch-src_plugins__3rdparty_umuscle_src_MuscleWorkPool.cpp
deleted file mode 100644
index 5a6131fbd06b..000000000000
--- a/biology/ugene/files/patch-src_plugins__3rdparty_umuscle_src_MuscleWorkPool.cpp
+++ /dev/null
@@ -1,14 +0,0 @@
---- src/plugins_3rdparty/umuscle/src/MuscleWorkPool.cpp.orig	2016-03-31 12:22:09 UTC
-+++ src/plugins_3rdparty/umuscle/src/MuscleWorkPool.cpp
-@@ -28,9 +28,10 @@ namespace U2 {
- 
-     MuscleWorkPool::MuscleWorkPool(MuscleContext *_ctx, const MuscleTaskSettings  &_config, TaskStateInfo& _ti, int _nThreads, const MAlignment& _ma, MAlignment& _res, bool _mhack)
-         :ctx(_ctx), config(_config), ma(_ma), res(_res), mhack(_mhack), Weights(NULL), ProgNodes(NULL), ph(NULL), ti(_ti),
--        treeNodeStatus(NULL), treeNodeIndexes(NULL), nThreads(_nThreads), uJoin(0), ptrbOscillating(false), bAnyAccepted(false), InternalNodeIndexes(NULL), uInternalNodeCount(0),
-+        treeNodeStatus(NULL), treeNodeIndexes(NULL), nThreads(_nThreads), uJoin(0), bAnyAccepted(false), InternalNodeIndexes(NULL), uInternalNodeCount(0),
-         bReversed(false), bRight(false), History(NULL), bLockLeft(NULL), bLockRight(false), msaIn(NULL)
-     {
-+            *ptrbOscillating = false;
-             refineConstructot();
-     }
-     MuscleWorkPool::~MuscleWorkPool() {
diff --git a/biology/ugene/files/patch-src_plugins__3rdparty_variants_variants.pri b/biology/ugene/files/patch-src_plugins__3rdparty_variants_variants.pri
deleted file mode 100644
index 9ecf2cc231fb..000000000000
--- a/biology/ugene/files/patch-src_plugins__3rdparty_variants_variants.pri
+++ /dev/null
@@ -1,11 +0,0 @@
---- src/plugins_3rdparty/variants/variants.pri.orig	2016-03-31 12:22:09 UTC
-+++ src/plugins_3rdparty/variants/variants.pri
-@@ -20,7 +20,7 @@ use_bundled_zlib() {
- win32 : LIBS += -lwsock32
- 
- 
--INCLUDEPATH += src ../../include /usr/include
-+INCLUDEPATH += src ../../include
- INCLUDEPATH += ../../libs_3rdparty/samtools/src/samtools 
- INCLUDEPATH += ../../libs_3rdparty/samtools/src
- INCLUDEPATH += ../../libs_3rdparty/samtools/src/samtools/bcftools
diff --git a/biology/ugene/files/patch-src_plugins__checker_src_Main.cpp b/biology/ugene/files/patch-src_plugins__checker_src_Main.cpp
index 44f703d392b2..bd0d64942c01 100644
--- a/biology/ugene/files/patch-src_plugins__checker_src_Main.cpp
+++ b/biology/ugene/files/patch-src_plugins__checker_src_Main.cpp
@@ -1,4 +1,4 @@
---- src/plugins_checker/src/Main.cpp.orig	2016-03-31 12:22:09 UTC
+--- src/plugins_checker/src/Main.cpp.orig	2018-08-16 13:59:06 UTC
 +++ src/plugins_checker/src/Main.cpp
 @@ -39,7 +39,7 @@
  #include <ServiceRegistryImpl.h>
@@ -20,7 +20,7 @@
  
      const char* build = QT_VERSION_STR, *runtime = qVersion();
      if (strcmp(build, runtime) > 0){
-@@ -140,7 +142,7 @@ int main(int argc, char **argv)
+@@ -141,7 +143,7 @@ int main(int argc, char **argv)
      delete cmdLineRegistry;
      appContext->setCMDLineRegistry(NULL);
  
diff --git a/biology/ugene/files/patch-src_ugene__globals.pri b/biology/ugene/files/patch-src_ugene__globals.pri
deleted file mode 100644
index 6c0a38639d38..000000000000
--- a/biology/ugene/files/patch-src_ugene__globals.pri
+++ /dev/null
@@ -1,13 +0,0 @@
---- src/ugene_globals.pri.orig	2016-03-31 12:22:21 UTC
-+++ src/ugene_globals.pri
-@@ -8,8 +8,8 @@ DEFINES+=UGENE_VER_MAJOR=$${UGENE_VER_MA
- DEFINES+=UGENE_VER_MINOR=$${UGENE_VER_MINOR}
- DEFINES+=UGENE_VER_PATCH=$${UGENE_VER_PATCH}
- 
--unix : !macx : INCLUDEPATH-=/usr/include
--unix : !macx : INCLUDEPATH+=/usr/include/qt5 /usr/include
-+#unix : !macx : INCLUDEPATH-=/usr/include
-+#unix : !macx : INCLUDEPATH+=/usr/include/qt5 /usr/include
- #unix : !macx : INCLUDEPATH =/usr/include/qt5 $$INCLUDEPATH
- 
- # NGS package
diff --git a/biology/ugene/files/patch-src_ugenecl_src_Main.cpp b/biology/ugene/files/patch-src_ugenecl_src_Main.cpp
index e932d4efa4c9..917fc096b4c4 100644
--- a/biology/ugene/files/patch-src_ugenecl_src_Main.cpp
+++ b/biology/ugene/files/patch-src_ugenecl_src_Main.cpp
@@ -1,6 +1,6 @@
---- src/ugenecl/src/Main.cpp.orig	2016-03-31 12:22:19 UTC
+--- src/ugenecl/src/Main.cpp.orig	2018-08-16 13:59:20 UTC
 +++ src/ugenecl/src/Main.cpp
-@@ -94,7 +94,7 @@
+@@ -93,7 +93,7 @@
  #include <ServiceRegistryImpl.h>
  #include <SettingsImpl.h>
  #include <TaskSchedulerImpl.h>
@@ -9,7 +9,7 @@
  
  // local project imports
  #include "DumpHelpTask.h"
-@@ -192,9 +192,11 @@ static void setSearchPaths() {
+@@ -191,6 +191,7 @@ static void setSearchPaths() {
  
  int main(int argc, char **argv)
  {
@@ -17,10 +17,14 @@
      if (CrashHandler::isEnabled()) {
          CrashHandler::setupHandler();
      }
+@@ -198,6 +199,7 @@ int main(int argc, char **argv)
+     if (qgetenv(ENV_SEND_CRASH_REPORTS) == "0") {
+         CrashHandler::setSendCrashReports(false);
+     }
 +#endif
+ 
      const char* build = QT_VERSION_STR, *runtime = qVersion();
      if (strcmp(build, runtime) > 0){
-         printf("Installed Qt version must be %s or greater \r\n", QT_VERSION_STR);
 @@ -617,7 +619,7 @@ int main(int argc, char **argv)
      delete pwr;
      appContext->setAlignmentAlgorithmsRegistry(NULL);
diff --git a/biology/ugene/files/patch-src_ugeneui_src_Main.cpp b/biology/ugene/files/patch-src_ugeneui_src_Main.cpp
index d968dad9c8d1..e5dcadcdea21 100644
--- a/biology/ugene/files/patch-src_ugeneui_src_Main.cpp
+++ b/biology/ugene/files/patch-src_ugeneui_src_Main.cpp
@@ -1,6 +1,6 @@
---- src/ugeneui/src/Main.cpp.orig	2016-03-31 12:22:18 UTC
+--- src/ugeneui/src/Main.cpp.orig	2018-08-16 13:59:19 UTC
 +++ src/ugeneui/src/Main.cpp
-@@ -134,7 +134,7 @@
+@@ -136,7 +136,7 @@
  #include <ServiceRegistryImpl.h>
  #include <SettingsImpl.h>
  #include <TaskSchedulerImpl.h>
@@ -9,7 +9,7 @@
  
  #include "app_settings/AppSettingsGUIImpl.h"
  #include "app_settings/logview_settings/LogSettingsGUIController.h"
-@@ -343,9 +343,11 @@ void fixMacFonts() {
+@@ -353,6 +353,7 @@ void fixMacFonts() {
  
  int main(int argc, char **argv)
  {
@@ -17,11 +17,15 @@
      if (CrashHandler::isEnabled()) {
          CrashHandler::setupHandler();
      }
+@@ -360,6 +361,7 @@ int main(int argc, char **argv)
+     if (qgetenv(ENV_SEND_CRASH_REPORTS) == "0") {
+         CrashHandler::setSendCrashReports(false);
+     }
 +#endif
  
      QT_REQUIRE_VERSION( argc, argv, QT_VERSION_STR );
  
-@@ -966,7 +968,7 @@ int main(int argc, char **argv)
+@@ -973,7 +975,7 @@ int main(int argc, char **argv)
      }
  
      UgeneUpdater::onClose();
diff --git a/biology/ugene/files/patch-ugene.pro b/biology/ugene/files/patch-ugene.pro
index 7a76899e33f1..8962a9edc02e 100644
--- a/biology/ugene/files/patch-ugene.pro
+++ b/biology/ugene/files/patch-ugene.pro
@@ -1,4 +1,4 @@
---- ugene.pro.orig	2016-03-31 12:21:56 UTC
+--- ugene.pro.orig	2018-08-16 13:58:51 UTC
 +++ ugene.pro
 @@ -20,7 +20,6 @@ use_bundled_zlib() {
  }
@@ -7,19 +7,20 @@
 -          src/libs_3rdparty/breakpad \
            src/libs_3rdparty/qscore \
            src/libs_3rdparty/sqlite3 \
-           src/libs_3rdparty/gtest \
-@@ -144,15 +143,8 @@ UGENE_TRANSL_QM_TARGET_DIR = $$OUT_PWD/s
+           src/libs_3rdparty/samtools \
+@@ -141,16 +140,8 @@ UGENE_TRANSL_QM_TARGET_DIR = $$OUT_PWD/src/_debug $$OU
  win32 : UGENE_DEV_NULL = nul
  unix : UGENE_DEV_NULL = /dev/null
  
 -UGENE_LRELEASE =
--UGENE_LUPDATE = 
--system(lrelease-qt5 -version > $$UGENE_DEV_NULL 2> $$UGENE_DEV_NULL) {
--    UGENE_LRELEASE = lrelease-qt5
--    UGENE_LUPDATE = lupdate-qt5
--} else : system(lrelease -version > $$UGENE_DEV_NULL 2> $$UGENE_DEV_NULL) {
--    UGENE_LRELEASE = lrelease
--    UGENE_LUPDATE = lupdate
+-UGENE_LUPDATE =
+-message(Using QT from $$[QT_INSTALL_BINS])
+-system($$[QT_INSTALL_BINS]/lrelease-qt5 -version > $$UGENE_DEV_NULL 2> $$UGENE_DEV_NULL) {
+-    UGENE_LRELEASE = $$[QT_INSTALL_BINS]/lrelease-qt5
+-    UGENE_LUPDATE = $$[QT_INSTALL_BINS]/lupdate-qt5
+-} else : system($$[QT_INSTALL_BINS]/lrelease -version > $$UGENE_DEV_NULL 2> $$UGENE_DEV_NULL) {
+-    UGENE_LRELEASE = $$[QT_INSTALL_BINS]/lrelease
+-    UGENE_LUPDATE = $$[QT_INSTALL_BINS]/lupdate
 -}
 +UGENE_LRELEASE = $$LRELEASE
 +UGENE_LUPDATE = $$LUPDATE
diff --git a/biology/ugene/pkg-plist b/biology/ugene/pkg-plist
index 89da368a2198..08b3c7f508f3 100644
--- a/biology/ugene/pkg-plist
+++ b/biology/ugene/pkg-plist
@@ -1,4 +1,8 @@
 bin/ugene
+lib/ugene/libQSpec.so
+lib/ugene/libQSpec.so.1
+lib/ugene/libQSpec.so.1.0
+lib/ugene/libQSpec.so.1.0.0
 lib/ugene/libU2Algorithm.so
 lib/ugene/libU2Algorithm.so.1
 lib/ugene/libU2Algorithm.so.1.0
@@ -27,10 +31,6 @@ lib/ugene/libU2Private.so
 lib/ugene/libU2Private.so.1
 lib/ugene/libU2Private.so.1.0
 lib/ugene/libU2Private.so.1.0.0
-lib/ugene/libU2Remote.so
-lib/ugene/libU2Remote.so.1
-lib/ugene/libU2Remote.so.1.0
-lib/ugene/libU2Remote.so.1.0.0
 lib/ugene/libU2Script.so
 lib/ugene/libU2Script.so.1
 lib/ugene/libU2Script.so.1.0
@@ -43,16 +43,14 @@ lib/ugene/libU2View.so
 lib/ugene/libU2View.so.1
 lib/ugene/libU2View.so.1.0
 lib/ugene/libU2View.so.1.0.0
-lib/ugene/libgtest.so
-lib/ugene/libgtest.so.1
-lib/ugene/libgtest.so.1.0
-lib/ugene/libgtest.so.1.0.0
 lib/ugene/libugenedb.so
 lib/ugene/libugenedb.so.1
 lib/ugene/libugenedb.so.1.0
 lib/ugene/libugenedb.so.1.0.0
 lib/ugene/plugins/CoreTests.license
 lib/ugene/plugins/CoreTests.plugin
+lib/ugene/plugins/GUITestBase.license
+lib/ugene/plugins/GUITestBase.plugin
 lib/ugene/plugins/annotator.license
 lib/ugene/plugins/annotator.plugin
 lib/ugene/plugins/api_tests.license
@@ -67,8 +65,12 @@ lib/ugene/plugins/chroma_view.license
 lib/ugene/plugins/chroma_view.plugin
 lib/ugene/plugins/circular_view.license
 lib/ugene/plugins/circular_view.plugin
+lib/ugene/plugins/clark_support.license
+lib/ugene/plugins/clark_support.plugin
 lib/ugene/plugins/dbi_bam.license
 lib/ugene/plugins/dbi_bam.plugin
+lib/ugene/plugins/diamond_support.license
+lib/ugene/plugins/diamond_support.plugin
 lib/ugene/plugins/dna_export.license
 lib/ugene/plugins/dna_export.plugin
 lib/ugene/plugins/dna_flexibility.license
@@ -89,14 +91,18 @@ lib/ugene/plugins/gor4.license
 lib/ugene/plugins/gor4.plugin
 lib/ugene/plugins/hmm2.license
 lib/ugene/plugins/hmm2.plugin
-%%SSE2%%lib/ugene/plugins/hmm3.license
-%%SSE2%%lib/ugene/plugins/hmm3.plugin
 lib/ugene/plugins/kalign.license
 lib/ugene/plugins/kalign.plugin
+lib/ugene/plugins/kraken_support.license
+lib/ugene/plugins/kraken_support.plugin
 lib/ugene/plugins/libCoreTests.so
 lib/ugene/plugins/libCoreTests.so.1
 lib/ugene/plugins/libCoreTests.so.1.0
 lib/ugene/plugins/libCoreTests.so.1.0.0
+lib/ugene/plugins/libGUITestBase.so
+lib/ugene/plugins/libGUITestBase.so.1
+lib/ugene/plugins/libGUITestBase.so.1.0
+lib/ugene/plugins/libGUITestBase.so.1.0.0
 lib/ugene/plugins/libannotator.so
 lib/ugene/plugins/libannotator.so.1
 lib/ugene/plugins/libannotator.so.1.0
@@ -125,10 +131,18 @@ lib/ugene/plugins/libcircular_view.so
 lib/ugene/plugins/libcircular_view.so.1
 lib/ugene/plugins/libcircular_view.so.1.0
 lib/ugene/plugins/libcircular_view.so.1.0.0
+lib/ugene/plugins/libclark_support.so
+lib/ugene/plugins/libclark_support.so.1
+lib/ugene/plugins/libclark_support.so.1.0
+lib/ugene/plugins/libclark_support.so.1.0.0
 lib/ugene/plugins/libdbi_bam.so
 lib/ugene/plugins/libdbi_bam.so.1
 lib/ugene/plugins/libdbi_bam.so.1.0
 lib/ugene/plugins/libdbi_bam.so.1.0.0
+lib/ugene/plugins/libdiamond_support.so
+lib/ugene/plugins/libdiamond_support.so.1
+lib/ugene/plugins/libdiamond_support.so.1.0
+lib/ugene/plugins/libdiamond_support.so.1.0.0
 lib/ugene/plugins/libdna_export.so
 lib/ugene/plugins/libdna_export.so.1
 lib/ugene/plugins/libdna_export.so.1.0
@@ -169,18 +183,22 @@ lib/ugene/plugins/libhmm2.so
 lib/ugene/plugins/libhmm2.so.1
 lib/ugene/plugins/libhmm2.so.1.0
 lib/ugene/plugins/libhmm2.so.1.0.0
-%%SSE2%%lib/ugene/plugins/libhmm3.so
-%%SSE2%%lib/ugene/plugins/libhmm3.so.1
-%%SSE2%%lib/ugene/plugins/libhmm3.so.1.0
-%%SSE2%%lib/ugene/plugins/libhmm3.so.1.0.0
 lib/ugene/plugins/libkalign.so
 lib/ugene/plugins/libkalign.so.1
 lib/ugene/plugins/libkalign.so.1.0
 lib/ugene/plugins/libkalign.so.1.0.0
+lib/ugene/plugins/libkraken_support.so
+lib/ugene/plugins/libkraken_support.so.1
+lib/ugene/plugins/libkraken_support.so.1.0
+lib/ugene/plugins/libkraken_support.so.1.0.0
 lib/ugene/plugins/liblinkdata_support.so
 lib/ugene/plugins/liblinkdata_support.so.1
 lib/ugene/plugins/liblinkdata_support.so.1.0
 lib/ugene/plugins/liblinkdata_support.so.1.0.0
+lib/ugene/plugins/libngs_reads_classification.so
+lib/ugene/plugins/libngs_reads_classification.so.1
+lib/ugene/plugins/libngs_reads_classification.so.1.0
+lib/ugene/plugins/libngs_reads_classification.so.1.0.0
 lib/ugene/plugins/libopencl_support.so
 lib/ugene/plugins/libopencl_support.so.1
 lib/ugene/plugins/libopencl_support.so.1.0
@@ -221,10 +239,6 @@ lib/ugene/plugins/libremote_blast.so
 lib/ugene/plugins/libremote_blast.so.1
 lib/ugene/plugins/libremote_blast.so.1.0
 lib/ugene/plugins/libremote_blast.so.1.0.0
-lib/ugene/plugins/libremote_service.so
-lib/ugene/plugins/libremote_service.so.1
-lib/ugene/plugins/libremote_service.so.1.0
-lib/ugene/plugins/libremote_service.so.1.0.0
 lib/ugene/plugins/librepeat_finder.so
 lib/ugene/plugins/librepeat_finder.so.1
 lib/ugene/plugins/librepeat_finder.so.1.0
@@ -241,10 +255,10 @@ lib/ugene/plugins/libtest_runner.so
 lib/ugene/plugins/libtest_runner.so.1
 lib/ugene/plugins/libtest_runner.so.1.0
 lib/ugene/plugins/libtest_runner.so.1.0.0
-%%NOX64%%lib/ugene/plugins/libumuscle.so
-%%NOX64%%lib/ugene/plugins/libumuscle.so.1
-%%NOX64%%lib/ugene/plugins/libumuscle.so.1.0
-%%NOX64%%lib/ugene/plugins/libumuscle.so.1.0.0
+lib/ugene/plugins/libumuscle.so
+lib/ugene/plugins/libumuscle.so.1
+lib/ugene/plugins/libumuscle.so.1.0
+lib/ugene/plugins/libumuscle.so.1.0.0
 lib/ugene/plugins/libvariants.so
 lib/ugene/plugins/libvariants.so.1
 lib/ugene/plugins/libvariants.so.1.0
@@ -253,12 +267,18 @@ lib/ugene/plugins/libweight_matrix.so
 lib/ugene/plugins/libweight_matrix.so.1
 lib/ugene/plugins/libweight_matrix.so.1.0
 lib/ugene/plugins/libweight_matrix.so.1.0.0
+lib/ugene/plugins/libwevote_support.so
+lib/ugene/plugins/libwevote_support.so.1
+lib/ugene/plugins/libwevote_support.so.1.0
+lib/ugene/plugins/libwevote_support.so.1.0.0
 lib/ugene/plugins/libworkflow_designer.so
 lib/ugene/plugins/libworkflow_designer.so.1
 lib/ugene/plugins/libworkflow_designer.so.1.0
 lib/ugene/plugins/libworkflow_designer.so.1.0.0
 lib/ugene/plugins/linkdata_support.license
 lib/ugene/plugins/linkdata_support.plugin
+lib/ugene/plugins/ngs_reads_classification.license
+lib/ugene/plugins/ngs_reads_classification.plugin
 lib/ugene/plugins/opencl_support.license
 lib/ugene/plugins/opencl_support.plugin
 lib/ugene/plugins/orf_marker.license
@@ -279,8 +299,6 @@ lib/ugene/plugins/query_designer.license
 lib/ugene/plugins/query_designer.plugin
 lib/ugene/plugins/remote_blast.license
 lib/ugene/plugins/remote_blast.plugin
-lib/ugene/plugins/remote_service.license
-lib/ugene/plugins/remote_service.plugin
 lib/ugene/plugins/repeat_finder.license
 lib/ugene/plugins/repeat_finder.plugin
 lib/ugene/plugins/sitecon.license
@@ -289,12 +307,14 @@ lib/ugene/plugins/smith_waterman.license
 lib/ugene/plugins/smith_waterman.plugin
 lib/ugene/plugins/test_runner.license
 lib/ugene/plugins/test_runner.plugin
-%%NOX64%%lib/ugene/plugins/umuscle.license
-%%NOX64%%lib/ugene/plugins/umuscle.plugin
+lib/ugene/plugins/umuscle.license
+lib/ugene/plugins/umuscle.plugin
 lib/ugene/plugins/variants.license
 lib/ugene/plugins/variants.plugin
 lib/ugene/plugins/weight_matrix.license
 lib/ugene/plugins/weight_matrix.plugin
+lib/ugene/plugins/wevote_support.license
+lib/ugene/plugins/wevote_support.plugin
 lib/ugene/plugins/workflow_designer.license
 lib/ugene/plugins/workflow_designer.plugin
 lib/ugene/plugins_checker
@@ -306,12 +326,18 @@ lib/ugene/ugenem
 lib/ugene/ugeneui
 man/man1/ugene.1.gz
 share/applications/ugene.desktop
-share/icons/application-x-ugene-ext.png
-share/mime/application-x-ugene.xml
+share/icons/hicolor/32x32/mimetypes/application-x-ugene-ext.png
+share/mime/packages/application-x-ugene.xml
 share/pixmaps/ugene.png
 share/pixmaps/ugene.xpm
 %%DATADIR%%/DBXRefRegistry.txt
 %%DATADIR%%/adapters/adapters.fasta
+%%DATADIR%%/adapters/illumina/NexteraPE-PE.fa
+%%DATADIR%%/adapters/illumina/TruSeq2-PE.fa
+%%DATADIR%%/adapters/illumina/TruSeq2-SE.fa
+%%DATADIR%%/adapters/illumina/TruSeq3-PE-2.fa
+%%DATADIR%%/adapters/illumina/TruSeq3-PE.fa
+%%DATADIR%%/adapters/illumina/TruSeq3-SE.fa
 %%DATADIR%%/back_translation/Bacteria/Arthrobacter_aurescens_TC1.cut
 %%DATADIR%%/back_translation/Bacteria/Bacillus_subtilis.cut
 %%DATADIR%%/back_translation/Bacteria/Escherichia_coli.cut
@@ -357,6 +383,7 @@ share/pixmaps/ugene.xpm
 %%DATADIR%%/cmdline/align-kalign.uwl
 %%DATADIR%%/cmdline/align-mafft.uwl
 %%DATADIR%%/cmdline/align-tcoffee.uwl
+%%DATADIR%%/cmdline/align-to-reference.uwl
 %%DATADIR%%/cmdline/align.uwl
 %%DATADIR%%/cmdline/convert-msa.uwl
 %%DATADIR%%/cmdline/convert-seq.uwl
@@ -372,6 +399,7 @@ share/pixmaps/ugene.xpm
 %%DATADIR%%/cmdline/generate-dna.uwl
 %%DATADIR%%/cmdline/hmm2-build.uwl
 %%DATADIR%%/cmdline/hmm2-search.uwl
+%%DATADIR%%/cmdline/hmm3-build-and-search.uwl
 %%DATADIR%%/cmdline/join-quality.uwl
 %%DATADIR%%/cmdline/local-blast+.uwl
 %%DATADIR%%/cmdline/local-blast.uwl
@@ -1150,6 +1178,8 @@ share/pixmaps/ugene.xpm
 %%DATADIR%%/samples/ABIF/A01.abi
 %%DATADIR%%/samples/ACE/BL060C3.ace
 %%DATADIR%%/samples/ACE/K26.ace
+%%DATADIR%%/samples/APR/DNA.apr
+%%DATADIR%%/samples/APR/gyrA.apr
 %%DATADIR%%/samples/Assembly/chrM.fa
 %%DATADIR%%/samples/Assembly/chrM.sam
 %%DATADIR%%/samples/Assembly/chrM.sorted.bam
@@ -1393,18 +1423,33 @@ share/pixmaps/ugene.xpm
 %%DATADIR%%/workflow_samples/Data merging/tfbs.uwl
 %%DATADIR%%/workflow_samples/HMMER/build-test-HMM.uwl
 %%DATADIR%%/workflow_samples/HMMER/searchHMM.uwl
-%%DATADIR%%/workflow_samples/NGS/assembly/spades_paired.uwl
-%%DATADIR%%/workflow_samples/NGS/assembly/spades_single.uwl
-%%DATADIR%%/workflow_samples/NGS/assembly.uwl
-%%DATADIR%%/workflow_samples/NGS/call_variants.uwl
 %%DATADIR%%/workflow_samples/NGS/chipseq_coverage.uwl
+%%DATADIR%%/workflow_samples/NGS/cistrome.uwl
 %%DATADIR%%/workflow_samples/NGS/cistrome/chip_seq.uwl
 %%DATADIR%%/workflow_samples/NGS/cistrome/chip_seq_with_control.uwl
-%%DATADIR%%/workflow_samples/NGS/cistrome.uwl
 %%DATADIR%%/workflow_samples/NGS/consensus.uwl
 %%DATADIR%%/workflow_samples/NGS/extract_coverage.uwl
 %%DATADIR%%/workflow_samples/NGS/extract_transcript_seq.uwl
 %%DATADIR%%/workflow_samples/NGS/fastqc.uwl
+%%DATADIR%%/workflow_samples/NGS/from_tools_menu_only/ngs_assembly.uwl
+%%DATADIR%%/workflow_samples/NGS/from_tools_menu_only/ngs_classification.uwl
+%%DATADIR%%/workflow_samples/NGS/ngs_assembly_illumina_pe.uwl
+%%DATADIR%%/workflow_samples/NGS/ngs_assembly_illumina_pe_nanopore.uwl
+%%DATADIR%%/workflow_samples/NGS/ngs_assembly_illumina_se.uwl
+%%DATADIR%%/workflow_samples/NGS/ngs_classification/ngs_classification_de_novo/ngs_classification_de_novo_paired.uwl
+%%DATADIR%%/workflow_samples/NGS/ngs_classification/ngs_classification_de_novo/ngs_classification_de_novo_single.uwl
+%%DATADIR%%/workflow_samples/NGS/ngs_classification/ngs_classification_parallel/ngs_classification_parallel_paired.uwl
+%%DATADIR%%/workflow_samples/NGS/ngs_classification/ngs_classification_parallel/ngs_classification_parallel_single.uwl
+%%DATADIR%%/workflow_samples/NGS/ngs_classification/ngs_classification_serial/ngs_classification_serial_paired.uwl
+%%DATADIR%%/workflow_samples/NGS/ngs_classification/ngs_classification_serial/ngs_classification_serial_single.uwl
+%%DATADIR%%/workflow_samples/NGS/ngs_classification_de_novo.uwl
+%%DATADIR%%/workflow_samples/NGS/ngs_classification_parallel.uwl
+%%DATADIR%%/workflow_samples/NGS/ngs_classification_serial.uwl
+%%DATADIR%%/workflow_samples/NGS/ngs_transcriptomics_tophat_stringtie.uwl
+%%DATADIR%%/workflow_samples/NGS/ngs_transcriptomics_tuxedo.uwl
+%%DATADIR%%/workflow_samples/NGS/ngs_variant_annotation.uwl
+%%DATADIR%%/workflow_samples/NGS/ngs_variant_calling.uwl
+%%DATADIR%%/workflow_samples/NGS/ngs_variant_calling_full.uwl
 %%DATADIR%%/workflow_samples/NGS/raw_chip.uwl
 %%DATADIR%%/workflow_samples/NGS/raw_dna.uwl
 %%DATADIR%%/workflow_samples/NGS/raw_ngs/chipseq/chipseq_paired.uwl
@@ -1422,9 +1467,7 @@ share/pixmaps/ugene.xpm
 %%DATADIR%%/workflow_samples/NGS/tuxedo/tuxedo_no_novel_transcr_paired.uwl
 %%DATADIR%%/workflow_samples/NGS/tuxedo/tuxedo_single_dataset.uwl
 %%DATADIR%%/workflow_samples/NGS/tuxedo/tuxedo_single_dataset_paired.uwl
-%%DATADIR%%/workflow_samples/NGS/tuxedo.uwl
 %%DATADIR%%/workflow_samples/NGS/unmapped_reads.uwl
-%%DATADIR%%/workflow_samples/NGS/variation_annotation.uwl
 %%DATADIR%%/workflow_samples/Sanger sequencing/trim-and-align.uwl
 %%DATADIR%%/workflow_samples/Scenarios/filter_matched.uwl
 %%DATADIR%%/workflow_samples/Scenarios/find_inverted_repeats.uwl
@@ -1432,6 +1475,7 @@ share/pixmaps/ugene.xpm
 %%DATADIR%%/workflow_samples/Scenarios/gene_by_gene_report.uwl
 %%DATADIR%%/workflow_samples/Scenarios/group_primers_pairs.uwl
 %%DATADIR%%/workflow_samples/Scenarios/intersect_annotations.uwl
+%%DATADIR%%/workflow_samples/Scenarios/length_filter.uwl
 %%DATADIR%%/workflow_samples/Scenarios/merge_sequence_annotation.uwl
 %%DATADIR%%/workflow_samples/Scenarios/pcr.uwl
 %%DATADIR%%/workflow_samples/Scenarios/remote_blasting.uwl
@@ -1442,6 +1486,7 @@ share/pixmaps/ugene.xpm
 %%DATADIR%%/workflow_samples/users/FASTQ Trimmer.usa
 %%DATADIR%%/workflow_samples/users/Get the first half of sequence.usa
 %%DATADIR%%/workflow_samples/users/Get the second half of sequence.usa
+%%DATADIR%%/workflow_samples/users/LengthMarker.usa
 %%DATADIR%%/workflow_samples/users/LinkData Fetch.usa
 %%DATADIR%%/workflow_samples/users/QualityFilter.usa
 %%DATADIR%%/workflow_samples/users/Read one sequence.usa