9 files changed, 204 insertions, 36 deletions

diff --git a/biology/ugene/Makefile b/biology/ugene/Makefile
index 88a5dfa468ea..8cd7c2e94c6f 100644
--- a/biology/ugene/Makefile
+++ b/biology/ugene/Makefile
@@ -2,8 +2,7 @@
 # $FreeBSD$
 
 PORTNAME=	ugene
-DISTVERSION=	1.17.0
-PORTREVISION=	1
+DISTVERSION=	1.22.0
 CATEGORIES=	biology science
 MASTER_SITES=	http://ugene.unipro.ru/downloads/
 DISTFILES=	${DISTNAME}${EXTRACT_SUFX} QueryDesigner_UserManual.pdf \
@@ -20,16 +19,13 @@ RUN_DEPENDS=	bash:shells/bash
 
 USES=		desktop-file-utils execinfo qmake
 USE_GL=		glu
-USE_QT4=	corelib gui network script webkit xml \
-		linguisttools_build moc_build qmake_build qtestlib_build \
-		rcc_build scripttools_build uic_build \
+USE_QT5=	buildtools_build linguisttools_build scripttools_build \
+		gui network printsupport script sql svg webkit widgets xml \
 		imageformats_run
-USE_XORG=	xtst
-USE_LDCONFIG=	yes
-INSTALLS_ICONS=	yes
 
 QMAKE_ARGS=	INSTALL_PREFIX="${PREFIX}" UGENE_INSTALL_DATA="${DATADIR}" \
-		INSTALL_MANDIR="${MAN1PREFIX}/man"
+		INSTALL_MANDIR="${MAN1PREFIX}/man" LRELEASE="${LRELEASE}" \
+		LUPDATE="${LUPDATE}"
 ALL_TARGET=	release
 
 DOCSDIR=	${DATADIR}/manuals
@@ -60,6 +56,7 @@ PLIST_SUB+=	SSE2="@comment "
 .endif
 
 post-extract:
+	@${MKDIR} ${WRKSRC}/data/manuals
 	${CP} -p ${_DISTDIR}/*.pdf ${WRKSRC}/data/manuals
 
 post-patch:
@@ -67,12 +64,14 @@ post-patch:
 	@${REINPLACE_CMD} -e 's|/bin/bash|/usr/bin/env bash|' \
 		${WRKSRC}/src/gen_bin_script.cmd \
 		${WRKSRC}/installer/_common_data/ugene
-	@${REINPLACE_CMD} -e 's|-bit version|& for ${OPSYS}|' \
+	@${REINPLACE_CMD} -e 's|-bit version|& for ${OPSYS}/${ARCH}|' \
 		${WRKSRC}/src/ugeneui/src/main_window/AboutDialogController.cpp
 	@${REINPLACE_CMD} -e '/unix_not_mac/,+11d' \
 		${WRKSRC}/src/corelibs/U2Core/U2Core.pri
-.for x in ugenecl ugeneui plugins_checker
-	@${ECHO_CMD} 'LIBS += -lexecinfo' >> ${WRKSRC}/src/${x}/${x}.pro
-.endfor
+	@${REINPLACE_CMD} 's, -lbreakpad,,' \
+		${WRKSRC}/src/corelibs/U2Private/U2Private.pri \
+		${WRKSRC}/src/plugins_checker/plugins_checker.pri \
+		${WRKSRC}/src/ugenecl/ugenecl.pri \
+		${WRKSRC}/src/ugeneui/ugeneui.pri
 
 .include <bsd.port.post.mk>
diff --git a/biology/ugene/distinfo b/biology/ugene/distinfo
index 09cac7bd1c3d..7d22d9d84ea9 100644
--- a/biology/ugene/distinfo
+++ b/biology/ugene/distinfo
@@ -1,8 +1,8 @@
-SHA256 (ugene/ugene-1.17.0.tar.gz) = d265a8a7d066e6cac2eeaa89645eb0ce1c0debeb9b321d80cea4a5595c082e08
-SIZE (ugene/ugene-1.17.0.tar.gz) = 20706555
-SHA256 (ugene/QueryDesigner_UserManual.pdf) = 17d7a68fdc9fc7ca2538c0b99a98a1f53cf664dc6207f98d9e4318eb35920847
-SIZE (ugene/QueryDesigner_UserManual.pdf) = 855679
-SHA256 (ugene/UniproUGENE_UserManual.pdf) = feee2712f81d24a84deb2f91fc0b13d64f051ff9c8b0129e862f8daafa8065a9
-SIZE (ugene/UniproUGENE_UserManual.pdf) = 13358880
-SHA256 (ugene/WorkflowDesigner_UserManual.pdf) = cc63575ccf85bf66ab8594c7209ee0628dd1a84165375f955eb5a191bbc5e233
-SIZE (ugene/WorkflowDesigner_UserManual.pdf) = 29393258
+SHA256 (ugene/ugene-1.22.0.tar.gz) = ee46be799c9f02a9b6a89f13747a4918d5c96c01676dc2d4cc4a4c98278912b6
+SIZE (ugene/ugene-1.22.0.tar.gz) = 20986853
+SHA256 (ugene/QueryDesigner_UserManual.pdf) = 5d232c0de7e9d1fd32b8ee0a78f9f4abe1ab9d6536ec3958c47de29f3096faf4
+SIZE (ugene/QueryDesigner_UserManual.pdf) = 855662
+SHA256 (ugene/UniproUGENE_UserManual.pdf) = ae6aef32a6e92a30ba7c36cdd894a8caf634d678f15da7ad9eab52b6f40b9ed6
+SIZE (ugene/UniproUGENE_UserManual.pdf) = 13443754
+SHA256 (ugene/WorkflowDesigner_UserManual.pdf) = 8cc6630f62c82de42926c14c3d01ebc3c7d85ab7d9ec2a81e55a19740806735c
+SIZE (ugene/WorkflowDesigner_UserManual.pdf) = 29474484
diff --git a/biology/ugene/files/patch-src_corelibs_U2Private_U2Private.pro b/biology/ugene/files/patch-src_corelibs_U2Private_U2Private.pro
new file mode 100644
index 000000000000..e75866cbf3c6
--- /dev/null
+++ b/biology/ugene/files/patch-src_corelibs_U2Private_U2Private.pro
@@ -0,0 +1,47 @@
+--- src/corelibs/U2Private/U2Private.pro.orig	2016-03-31 12:22:14 UTC
++++ src/corelibs/U2Private/U2Private.pro
+@@ -12,12 +12,7 @@ HEADERS += src/AppContextImpl.h \
+            src/PluginSupportImpl.h \
+            src/ServiceRegistryImpl.h \
+            src/SettingsImpl.h \
+-           src/TaskSchedulerImpl.h \
+-           src/crash_handler/CrashHandler.h \
+-           src/crash_handler/CrashHandlerArgsHelper.h \
+-           src/crash_handler/CrashHandlerPrivate.h \
+-           src/crash_handler/CrashLogCache.h \
+-           src/crash_handler/StackWalker.h
++           src/TaskSchedulerImpl.h
+ 
+ SOURCES += src/AppContextImpl.cpp \
+            src/AppSettingsImpl.cpp \
+@@ -30,29 +25,7 @@ SOURCES += src/AppContextImpl.cpp \
+            src/PluginSupportImpl.cpp \
+            src/ServiceRegistryImpl.cpp \
+            src/SettingsImpl.cpp \
+-           src/TaskSchedulerImpl.cpp \
+-           src/crash_handler/CrashHandler.cpp \
+-           src/crash_handler/CrashHandlerArgsHelper.cpp \
+-           src/crash_handler/CrashHandlerPrivate.cpp \
+-           src/crash_handler/CrashLogCache.cpp \
+-           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
+-}
+-
+-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
+-}
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
new file mode 100644
index 000000000000..5a6131fbd06b
--- /dev/null
+++ b/biology/ugene/files/patch-src_plugins__3rdparty_umuscle_src_MuscleWorkPool.cpp
@@ -0,0 +1,14 @@
+--- 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__checker_src_Main.cpp b/biology/ugene/files/patch-src_plugins__checker_src_Main.cpp
new file mode 100644
index 000000000000..44f703d392b2
--- /dev/null
+++ b/biology/ugene/files/patch-src_plugins__checker_src_Main.cpp
@@ -0,0 +1,31 @@
+--- src/plugins_checker/src/Main.cpp.orig	2016-03-31 12:22:09 UTC
++++ src/plugins_checker/src/Main.cpp
+@@ -39,7 +39,7 @@
+ #include <ServiceRegistryImpl.h>
+ #include <SettingsImpl.h>
+ #include <TaskSchedulerImpl.h>
+-#include <crash_handler/CrashHandler.h>
++//#include <crash_handler/CrashHandler.h>
+ 
+ #define TR_SETTINGS_ROOT QString("test_runner/")
+ 
+@@ -55,8 +55,10 @@ static void registerCoreServices() {
+ 
+ int main(int argc, char **argv)
+ {
++#if 0
+     CrashHandler::setupHandler();
+     CrashHandler::setSendCrashReports(false);
++#endif
+ 
+     const char* build = QT_VERSION_STR, *runtime = qVersion();
+     if (strcmp(build, runtime) > 0){
+@@ -140,7 +142,7 @@ int main(int argc, char **argv)
+     delete cmdLineRegistry;
+     appContext->setCMDLineRegistry(NULL);
+ 
+-    CrashHandler::shutdown();
++    //CrashHandler::shutdown();
+ 
+     return rc;
+ }
diff --git a/biology/ugene/files/patch-src_ugenecl_src_Main.cpp b/biology/ugene/files/patch-src_ugenecl_src_Main.cpp
new file mode 100644
index 000000000000..e932d4efa4c9
--- /dev/null
+++ b/biology/ugene/files/patch-src_ugenecl_src_Main.cpp
@@ -0,0 +1,32 @@
+--- src/ugenecl/src/Main.cpp.orig	2016-03-31 12:22:19 UTC
++++ src/ugenecl/src/Main.cpp
+@@ -94,7 +94,7 @@
+ #include <ServiceRegistryImpl.h>
+ #include <SettingsImpl.h>
+ #include <TaskSchedulerImpl.h>
+-#include <crash_handler/CrashHandler.h>
++//#include <crash_handler/CrashHandler.h>
+ 
+ // local project imports
+ #include "DumpHelpTask.h"
+@@ -192,9 +192,11 @@ static void setSearchPaths() {
+ 
+ int main(int argc, char **argv)
+ {
++#if 0
+     if (CrashHandler::isEnabled()) {
+         CrashHandler::setupHandler();
+     }
++#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);
+ 
+-    CrashHandler::shutdown();
++    //CrashHandler::shutdown();
+ 
+     return rc;
+ }
diff --git a/biology/ugene/files/patch-src_ugeneui_src_Main.cpp b/biology/ugene/files/patch-src_ugeneui_src_Main.cpp
new file mode 100644
index 000000000000..d968dad9c8d1
--- /dev/null
+++ b/biology/ugene/files/patch-src_ugeneui_src_Main.cpp
@@ -0,0 +1,32 @@
+--- src/ugeneui/src/Main.cpp.orig	2016-03-31 12:22:18 UTC
++++ src/ugeneui/src/Main.cpp
+@@ -134,7 +134,7 @@
+ #include <ServiceRegistryImpl.h>
+ #include <SettingsImpl.h>
+ #include <TaskSchedulerImpl.h>
+-#include <crash_handler/CrashHandler.h>
++//#include <crash_handler/CrashHandler.h>
+ 
+ #include "app_settings/AppSettingsGUIImpl.h"
+ #include "app_settings/logview_settings/LogSettingsGUIController.h"
+@@ -343,9 +343,11 @@ void fixMacFonts() {
+ 
+ int main(int argc, char **argv)
+ {
++#if 0
+     if (CrashHandler::isEnabled()) {
+         CrashHandler::setupHandler();
+     }
++#endif
+ 
+     QT_REQUIRE_VERSION( argc, argv, QT_VERSION_STR );
+ 
+@@ -966,7 +968,7 @@ int main(int argc, char **argv)
+     }
+ 
+     UgeneUpdater::onClose();
+-    CrashHandler::shutdown();
++    //CrashHandler::shutdown();
+ 
+     return rc;
+ }
diff --git a/biology/ugene/files/patch-ugene.pro b/biology/ugene/files/patch-ugene.pro
new file mode 100644
index 000000000000..7a76899e33f1
--- /dev/null
+++ b/biology/ugene/files/patch-ugene.pro
@@ -0,0 +1,28 @@
+--- ugene.pro.orig	2016-03-31 12:21:56 UTC
++++ ugene.pro
+@@ -20,7 +20,6 @@ use_bundled_zlib() {
+ }
+ 
+ SUBDIRS += \
+-          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 = $$OUT_PWD/s
+ win32 : UGENE_DEV_NULL = nul
+ unix : UGENE_DEV_NULL = /dev/null
+ 
+-UGENE_LRELEASE =
+-UGENE_LUPDATE = 
+-system(lrelease-qt5 -version > $$UGENE_DEV_NULL 2> $$UGENE_DEV_NULL) {
+-    UGENE_LRELEASE = lrelease-qt5
+-    UGENE_LUPDATE = lupdate-qt5
+-} else : system(lrelease -version > $$UGENE_DEV_NULL 2> $$UGENE_DEV_NULL) {
+-    UGENE_LRELEASE = lrelease
+-    UGENE_LUPDATE = lupdate
+-}
++UGENE_LRELEASE = $$LRELEASE
++UGENE_LUPDATE = $$LUPDATE
+ 
+ #foreach 'language'
+ for( i, UGENE_TRANSL_IDX ) {
diff --git a/biology/ugene/pkg-plist b/biology/ugene/pkg-plist
index 33f061e4a730..89da368a2198 100644
--- a/biology/ugene/pkg-plist
+++ b/biology/ugene/pkg-plist
@@ -53,8 +53,6 @@ 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
@@ -83,8 +81,6 @@ lib/ugene/plugins/dotplot.license
 lib/ugene/plugins/dotplot.plugin
 lib/ugene/plugins/enzymes.license
 lib/ugene/plugins/enzymes.plugin
-lib/ugene/plugins/expert_discovery.license
-lib/ugene/plugins/expert_discovery.plugin
 lib/ugene/plugins/external_tool_support.license
 lib/ugene/plugins/external_tool_support.plugin
 lib/ugene/plugins/genome_aligner.license
@@ -101,10 +97,6 @@ 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
@@ -161,10 +153,6 @@ lib/ugene/plugins/libenzymes.so
 lib/ugene/plugins/libenzymes.so.1
 lib/ugene/plugins/libenzymes.so.1.0
 lib/ugene/plugins/libenzymes.so.1.0.0
-lib/ugene/plugins/libexpert_discovery.so
-lib/ugene/plugins/libexpert_discovery.so.1
-lib/ugene/plugins/libexpert_discovery.so.1.0
-lib/ugene/plugins/libexpert_discovery.so.1.0.0
 lib/ugene/plugins/libexternal_tool_support.so
 lib/ugene/plugins/libexternal_tool_support.so.1
 lib/ugene/plugins/libexternal_tool_support.so.1.0
@@ -310,10 +298,8 @@ lib/ugene/plugins/weight_matrix.plugin
 lib/ugene/plugins/workflow_designer.license
 lib/ugene/plugins/workflow_designer.plugin
 lib/ugene/plugins_checker
-lib/ugene/transl_cs.qm
 lib/ugene/transl_en.qm
 lib/ugene/transl_ru.qm
-lib/ugene/transl_zh.qm
 lib/ugene/ugene
 lib/ugene/ugenecl
 lib/ugene/ugenem
@@ -374,7 +360,6 @@ share/pixmaps/ugene.xpm
 %%DATADIR%%/cmdline/align.uwl
 %%DATADIR%%/cmdline/convert-msa.uwl
 %%DATADIR%%/cmdline/convert-seq.uwl
-%%DATADIR%%/cmdline/das_annotation.uwl
 %%DATADIR%%/cmdline/extract-sequence.uwl
 %%DATADIR%%/cmdline/extract_consensus_sequence.uwl
 %%DATADIR%%/cmdline/extract_consensus_string.uwl