- Update to version 1.13.0 and improve FreeBSD support; it also builds

  pretty cleanly with GCC v4.2, v4.6, and Clang (modulo a few warnings)
- Sadly, do not use PORTDOCS: since DOCSDIR is set to be inside DATADIR,
  and will get appended to PLIST after @dirrm %%DATADIR%%, which upsets
  sanity checking tools; instead, list the docs explicitly in DISTFILES
  and add them to pkg-plist (guarded by %%PORTDOCS%%)

Tested on:	i386 (only)

9 files changed, 378 insertions, 140 deletions

diff --git a/biology/ugene/Makefile b/biology/ugene/Makefile
index 84935410684..48a450bb3de 100644
--- a/biology/ugene/Makefile
+++ b/biology/ugene/Makefile
@@ -2,10 +2,11 @@
 # $FreeBSD$
 
 PORTNAME=	ugene
-DISTVERSION=	1.12.3
+DISTVERSION=	1.13.0
 CATEGORIES=	biology
 MASTER_SITES=	http://ugene.unipro.ru/downloads/
-DISTFILES=	${DISTNAME}${EXTRACT_SUFX} ${PORTDOCS}
+DISTFILES=	${DISTNAME}${EXTRACT_SUFX} QueryDesigner_UserManual.pdf \
+		UniproUGENE_UserManual.pdf WorkflowDesigner_UserManual.pdf
 DIST_SUBDIR=	${PORTNAME}
 EXTRACT_ONLY=	${DISTNAME}${EXTRACT_SUFX}
 
@@ -22,7 +23,8 @@ RUN_DEPENDS=	bash:${PORTSDIR}/shells/bash
 USES=		qmake
 USE_GL=		glu
 USE_QT4=	gui webkit xml svg linguist_build moc_build qmake_build \
-		qtestlib_build rcc_build uic_build imageformats_run
+		qtestlib_build rcc_build uic_build imageformats_run \
+		scripttools_build
 USE_XORG=	xtst
 USE_LDCONFIG=	yes
 INSTALLS_ICONS=	yes
@@ -32,14 +34,13 @@ QMAKE_ARGS=	INSTALL_PREFIX=${PREFIX} UGENE_INSTALL_DATA=${DATADIR} \
 ALL_TARGET=	release
 
 DOCSDIR=	${DATADIR}/manuals
-PORTDOCS=	QueryDesigner_UserManual.pdf UniproUGENE_UserManual.pdf \
-		WorkflowDesigner_UserManual.pdf
 
 OPTIONS_DEFINE=	DOCS
 DOCS_DESC=	Install official UGENE documentation (PDF)
 
 .include <bsd.port.pre.mk>
 
+# Required for Google Test code
 .if ${OSVERSION} > 1000054
 CXXFLAGS+=	-std=c++11
 .endif
@@ -64,10 +65,36 @@ post-patch:
 	@${REINPLACE_CMD} -e 's|/bin/bash|/usr/bin/env bash|' \
 		${WRKSRC}/src/gen_bin_script.cmd \
 		${WRKSRC}/installer/_common_data/ugene
-# remove BOM from files and non-latin comments; gcc 4.2 does not like them
-	@${REINPLACE_CMD} -e '1s|^[^/]*|| ; /lose sequence view,/d' \
-		${WRKSRC}/src/plugins/GUITestBase/src/tests/common_scenarios/smith_waterman_dialog/GTTestsSWDialog.cpp \
-		${WRKSRC}/src/plugins/GUITestBase/src/tests/common_scenarios/repeat_finder/GTTestsRepeatFinder.cpp
+	@${REINPLACE_CMD} -e '30s|^|#include <time.h>|' \
+		${WRKSRC}/src/plugins/dbi_bam/src/BAMDbiPlugin.h
+	@${REINPLACE_CMD} -e 's|runTime=NULL|runTime=0|' \
+		${WRKSRC}/src/plugins/test_runner/src/TestViewReporter.h
+	@${REINPLACE_CMD} -e 's|Q_OS_LINUX|Q_OS_UNIX|' \
+		${WRKSRC}/src/ugenem/src/main.cpp
+	@(cd ${WRKSRC}/src/plugins/external_tool_support/src && \
+		${REINPLACE_CMD} -e 's/LINUX) || defined(Q_OS_MAC/UNIX/' \
+			ExternalToolSupportPlugin.cpp \
+			R/RSupport.cpp \
+			blast/BlastAllSupport.cpp \
+			blast/FormatDBSupport.cpp \
+			blast_plus/BlastDBCmdSupport.cpp \
+			blast_plus/BlastPlusSupport.cpp \
+			bowtie/BowtieSupport.cpp \
+			bowtie2/Bowtie2Support.cpp \
+			bwa/BwaSupport.cpp \
+			cap3/CAP3Support.cpp \
+			clustalo/ClustalOSupport.cpp \
+			clustalw/ClustalWSupport.cpp \
+			cufflinks/CufflinksSupport.cpp \
+			mrbayes/MrBayesSupport.cpp \
+			perl/PerlSupport.cpp \
+			python/PythonSupport.cpp \
+			samtools/BcfToolsSupport.cpp \
+			samtools/SamToolsExtToolSupport.cpp \
+			spidey/SpideySupport.cpp \
+			tcoffee/TCoffeeSupport.cpp \
+			tophat/TopHatSupport.cpp \
+			utils/ExternalToolSearchTask.cpp)
 
 post-configure:
 	@${REINPLACE_CMD} -e '/^LFLAGS/s,-pthread,-lexecinfo &,' \
diff --git a/biology/ugene/distinfo b/biology/ugene/distinfo
index f98ab73b082..b3af3225c50 100644
--- a/biology/ugene/distinfo
+++ b/biology/ugene/distinfo
@@ -1,5 +1,5 @@
-SHA256 (ugene/ugene-1.12.3.tar.gz) = 6642ec6ef5110b50b38c9620be4a98101d9a7b325a61a202ee7e0f2c67d45496
-SIZE (ugene/ugene-1.12.3.tar.gz) = 17611949
+SHA256 (ugene/ugene-1.13.0.tar.gz) = 65bd8c343bb18a2aece4b0b9f703435727f1523b5a7344f43fe5e176b9428a3f
+SIZE (ugene/ugene-1.13.0.tar.gz) = 19079436
 SHA256 (ugene/QueryDesigner_UserManual.pdf) = 3c5bd735c02b7ac24bd319823fde2d175b750adc1c37fe7b17e2009452a00ddd
 SIZE (ugene/QueryDesigner_UserManual.pdf) = 1306825
 SHA256 (ugene/UniproUGENE_UserManual.pdf) = 6c682c86f47a4c337eb4acdf0ae23ffa1b7fef1337d11e631655bfc943167b46
diff --git a/biology/ugene/files/patch-clang-fixes b/biology/ugene/files/patch-clang-fixes
deleted file mode 100644
index 3abf7b57fed..00000000000
--- a/biology/ugene/files/patch-clang-fixes
+++ /dev/null
@@ -1,91 +0,0 @@
---- src/corelibs/U2Gui/src/util/ProjectTreeController.cpp.orig	2013-10-08 15:07:58.000000000 +0800
-+++ src/corelibs/U2Gui/src/util/ProjectTreeController.cpp	2013-10-30 19:47:27.000000000 +0800
-@@ -448,7 +448,7 @@ void ProjectTreeController::sl_onCloseEd
-             QMessageBox::critical(0, "Error", tr("Duplicate object names are not allowed"));
-             return;
- 
--        } else if (newName.contains(invalidCharactersRegExp) != NULL) {
-+        } else if (newName.contains(invalidCharactersRegExp) != false) {
-             QMessageBox::critical(0, "Error", tr("The name can't contain any of the following characters: %1").arg(invalidCharacters));
-             return;
-         }
---- src/corelibs/U2Private/src/CrashHandler.cpp.orig	2013-10-08 15:07:59.000000000 +0800
-+++ src/corelibs/U2Private/src/CrashHandler.cpp	2013-10-30 19:18:30.000000000 +0800
-@@ -349,7 +349,7 @@ void CrashHandler::setupHandler() {
- #define SA_FLAGS (SA_ONSTACK | SA_SIGINFO)
- 
-     stack_t sigstk;
--    sigstk.ss_sp = malloc(SIGSTKSZ * 2);
-+    sigstk.ss_sp = static_cast<char *>(malloc(SIGSTKSZ * 2));
-     sigstk.ss_size = SIGSTKSZ * 2;
-     sigstk.ss_flags = 0;
-     if (sigaltstack(&sigstk,0) < 0) {
---- src/plugins/biostruct3d_view/src/MolecularSurfaceRenderer.cpp.orig	2013-10-08 15:07:39.000000000 +0800
-+++ src/plugins/biostruct3d_view/src/MolecularSurfaceRenderer.cpp	2013-10-30 21:42:54.000000000 +0800
-@@ -80,9 +80,21 @@ void DotsRenderer::drawSurface( Molecula
-     glBegin(GL_POINTS);
-     foreach(const Face& face, surface.getFaces()) {
-         float vct[3][3] = {
--            {face.v[0].x,face.v[0].y,face.v[0].z},
--            {face.v[1].x,face.v[1].y,face.v[1].z},
--            {face.v[2].x,face.v[2].y,face.v[2].z},
-+            {
-+                static_cast<float>(face.v[0].x),
-+                static_cast<float>(face.v[0].y),
-+                static_cast<float>(face.v[0].z),
-+            },
-+            {
-+                static_cast<float>(face.v[1].x),
-+                static_cast<float>(face.v[1].y),
-+                static_cast<float>(face.v[1].z),
-+            },
-+            {
-+                static_cast<float>(face.v[2].x),
-+                static_cast<float>(face.v[2].y),
-+                static_cast<float>(face.v[2].z),
-+            },
-         };
-         glVertex3fv(vct[0]);
-         glVertex3fv(vct[1]);
---- src/plugins/expert_discovery/src/ExpertDiscoveryTreeWidgetsCtrl.cpp.orig	2013-10-08 15:07:42.000000000 +0800
-+++ src/plugins/expert_discovery/src/ExpertDiscoveryTreeWidgetsCtrl.cpp	2013-10-30 22:02:40.000000000 +0800
-@@ -198,7 +198,7 @@ void EDProjectTree::updateSequenceBase(E
- void EDProjectTree::sl_propChanged(EDProjectItem* item, const EDPIProperty* prop, QString newVal){
-     switch (item->getType()) {
-         case PIT_CS_FOLDER: 
--            if (prop->getName().compare("Name", Qt::CaseInsensitive) == NULL) {
-+            if (prop->getName().compare("Name", Qt::CaseInsensitive) == 0) {
-                 EDPICSDirectory* pPI = dynamic_cast<EDPICSDirectory*>(item);
-                 CSFolder* pFolder = findFolder(pPI);
-                 const CSFolder* pParentFolder = pFolder->getParentFolder();
---- src/plugins/test_runner/src/TestViewReporter.h.orig	2013-10-08 15:07:45.000000000 +0800
-+++ src/plugins/test_runner/src/TestViewReporter.h	2013-10-30 21:50:12.000000000 +0800
-@@ -44,7 +44,7 @@ namespace U2 {
- 
-  public:
- 
--    TestViewReporter(TestViewController* parent,QTreeWidget* tree=NULL,int runTime=NULL);
-+    TestViewReporter(TestViewController* parent,QTreeWidget* tree=NULL,int runTime=0);
-     QString getReportText() {return curReportText;}
-     bool saveAs(const QString url,const QString data);
- 
-@@ -52,7 +52,7 @@ namespace U2 {
-     virtual void setupViewMenu(QMenu* n);
-  
-  private:
--    const QString prepareHTMLText(QTreeWidget* tree=NULL,int runTime=NULL);
-+    const QString prepareHTMLText(QTreeWidget* tree=NULL,int runTime=0);
-      
-     const QString getHTMLNoTests();
-     const QString getHTMLHead();
---- src/plugins_3rdparty/ball/src/source/COMMON/version.cpp.orig	2013-10-08 15:07:47.000000000 +0800
-+++ src/plugins_3rdparty/ball/src/source/COMMON/version.cpp	2013-10-30 21:20:22.000000000 +0800
-@@ -12,7 +12,7 @@ namespace BALL
- {
- 	const char* VersionInfo::getVersion() throw()
- 	{
--		return BALL_RELEASE_STRING " ("__DATE__", " __TIME__ ")";
-+		return BALL_RELEASE_STRING " (" __DATE__ ", " __TIME__ ")";
- 	}
- 
- 	int VersionInfo::getMinorRevision() throw(Exception::InvalidFormat)
diff --git a/biology/ugene/files/patch-gtest-std::tr1::tuple-fix b/biology/ugene/files/patch-gtest-std::tr1::tuple-fix
deleted file mode 100644
index 655f6c86d15..00000000000
--- a/biology/ugene/files/patch-gtest-std::tr1::tuple-fix
+++ /dev/null
@@ -1,34 +0,0 @@
-commit 23699acca083589be9dc3b6e8e5c5d09f654648d
-Author: marina.kolpakova <marina.kolpakova@itseez.com>
-Date:   Mon Oct 8 02:37:22 2012 +0400
-
-    fix for bug 2264
-    
-    fix compilation OpenCV with cxx11 under Ubuntu with clang and gcc 4.7
-
-diff --git a/modules/ts/include/opencv2/ts/ts_gtest.h b/modules/ts/include/opencv2/ts/ts_gtest.h
-index f98f71b..42eb608 100644
---- src/libs_3rdparty/gtest/src/gtest/internal/gtest-port.h.orig
-+++ src/libs_3rdparty/gtest/src/gtest/internal/gtest-port.h
-@@ -1654,7 +1654,21 @@ inline bool operator!=(const GTEST_10_TUPLE_(T)& t,
- #   undef _TR1_FUNCTIONAL  // Allows the user to #include
-                         // <tr1/functional> if he chooses to.
- #  else
-+#  if defined (__cplusplus) && __cplusplus > 199711L
-+#   include <tuple>
-+namespace std {
-+    namespace tr1 {
-+        using std::tuple;
-+        using std::tuple_element;
-+        using std::get;
-+        using std::tuple_size;
-+        using std::make_tuple;
-+    }
-+}
-+#  else
- #   include <tr1/tuple>  // NOLINT
-+#  endif
-+
- #  endif  // !GTEST_HAS_RTTI && GTEST_GCC_VER_ < 40302
- 
- # else
diff --git a/biology/ugene/files/patch-src-corelibs-U2Core-src-globals-AppResources.cpp b/biology/ugene/files/patch-src-corelibs-U2Core-src-globals-AppResources.cpp
new file mode 100644
index 00000000000..0f3304f9f73
--- /dev/null
+++ b/biology/ugene/files/patch-src-corelibs-U2Core-src-globals-AppResources.cpp
@@ -0,0 +1,73 @@
+--- src/corelibs/U2Core/src/globals/AppResources.cpp.orig
++++ src/corelibs/U2Core/src/globals/AppResources.cpp
+@@ -35,6 +35,10 @@
+ #include <proc/readproc.h>
+ #endif
+ 
++#if defined(Q_OS_LINUX) || defined(Q_OS_FREEBSD)
++#include <unistd.h> // for sysconf(3) and getpid(2)
++#endif
++
+ #ifdef Q_OS_WIN
+ #include <windows.h>
+ #include <Psapi.h>
+@@ -88,17 +92,15 @@ int AppResourcePool::getTotalPhysicalMem
+         coreLog.error("Total physical memory: getting info error");
+     }
+ 
+-#elif defined(Q_OS_LINUX)
+-    QProcess p;
+-    p.start("awk", QStringList() << "/MemTotal/ {print $2}" << "/proc/meminfo");
+-    p.waitForFinished();
+-    QString memory = p.readAllStandardOutput();
+-    p.close();
+-    bool ok = false;
+-    qlonglong output_mem = memory.toLongLong(&ok);
+-    if (ok) {
+-        totalPhysicalMemory = output_mem / 1024;
+-    }
++#elif defined(Q_OS_LINUX) || defined(Q_OS_FREEBSD)
++    long pagesize = sysconf(_SC_PAGESIZE);
++    long numpages = sysconf(_SC_PHYS_PAGES);
++
++    // Assume that page size is always a multiple of 1024, so it can be
++    // divided without losing any precision.  On the other hand, number
++    // of pages would hardly overflow `long' when multiplied by a small
++    // number (number of pages / 1024), so we should be safe here.
++    totalPhysicalMemory = (int)(numpages * (pagesize / 1024) / 1024);
+ 
+ #elif defined(Q_OS_MAC)
+ // TODO
+@@ -143,15 +145,27 @@ void AppResourcePool::setMaxMemorySizeIn
+ 
+ size_t AppResourcePool::getCurrentAppMemory() {
+ 
+-#ifdef Q_OS_LINUX
+-    struct proc_t usage;
+-    //look_up_our_self(&usage);
+-    return usage.vsize;
+-#endif
+ #ifdef Q_OS_WIN32
+     PROCESS_MEMORY_COUNTERS memCounter;
+     bool result = GetProcessMemoryInfo(GetCurrentProcess(), &memCounter, sizeof( memCounter ));
+     return memCounter.WorkingSetSize;
++#elif defined(Q_OS_LINUX)
++    struct proc_t usage;
++    //look_up_our_self(&usage);
++    return usage.vsize;
++#elif defined(Q_OS_FREEBSD)
++     QProcess p;
++     p.start("ps", QStringList() << "-o" << "vsize=" << "-p" << QString("%1").arg(getpid()));
++     p.waitForFinished();
++     QString ps_vsize = p.readAllStandardOutput();
++     p.close();
++     bool ok = false;
++     qlonglong output_mem = ps_vsize.toLongLong(&ok);
++     if (ok) {
++         return output_mem / 1024;
++     }
++#else
++    coreLog.error("Current application memory: Unsupported OS");
+ #endif
+ }
+ 
diff --git a/biology/ugene/files/patch-src-shtirlitz-Shtirlitz.cpp b/biology/ugene/files/patch-src-shtirlitz-Shtirlitz.cpp
new file mode 100644
index 00000000000..86be6655da1
--- /dev/null
+++ b/biology/ugene/files/patch-src-shtirlitz-Shtirlitz.cpp
@@ -0,0 +1,14 @@
+--- src/ugeneui/src/shtirlitz/Shtirlitz.cpp.orig
++++ src/ugeneui/src/shtirlitz/Shtirlitz.cpp
+@@ -239,7 +239,10 @@ void Shtirlitz::getOsNameAndVersion( QSt
+     version = QString::number(QSysInfo::MacintoshVersion);
+ #elif defined(Q_OS_LINUX)
+     name = "Linux";
+-    Q_UNUSED(version);//no version is available :(
++    Q_UNUSED(version);	//no version is available :(
++#elif defined(Q_OS_FREEBSD)
++    name = "FreeBSD";
++    Q_UNUSED(version);	//no version is available :(
+ #else
+     name = "Other";
+ #endif
diff --git a/biology/ugene/files/patch-src-ugenem-src-SendReportDialog.cpp b/biology/ugene/files/patch-src-ugenem-src-SendReportDialog.cpp
new file mode 100644
index 00000000000..7f75a92202e
--- /dev/null
+++ b/biology/ugene/files/patch-src-ugenem-src-SendReportDialog.cpp
@@ -0,0 +1,49 @@
+--- src/ugenem/src/SendReportDialog.cpp.orig
++++ src/ugenem/src/SendReportDialog.cpp
+@@ -44,6 +44,10 @@
+ #include <Winbase.h> //for IsProcessorFeaturePresent
+ #endif
+ 
++#if defined(Q_OS_LINUX) || defined(Q_OS_FREEBSD)
++#include <unistd.h> // for sysconf(3)
++#endif
++
+ #define HOST_URL "http://ugene.unipro.ru"
+ //#define HOST_URL "http://127.0.0.1"
+ #define DESTINATION_URL_KEEPER_PAGE "/crash_reports_dest.html"
+@@ -241,6 +245,8 @@ QString ReportSender::getOSVersion() {
+ 
+ #elif defined(Q_OS_LINUX)
+     result = "Linux";
++#elif defined(Q_OS_FREEBSD)
++    result = "FreeBSD";
+ #elif defined(Q_OS_MAC)
+     result = "Mac ";
+     switch (QSysInfo::MacintoshVersion){
+@@ -304,17 +310,15 @@ int ReportSender::getTotalPhysicalMemory
+         totalPhysicalMemory = memory_status.ullTotalPhys / (1024 * 1024);
+     }
+ 
+-#elif defined(Q_OS_LINUX)
+-    QProcess p;
+-    p.start("awk", QStringList() << "/MemTotal/ {print $2}" << "/proc/meminfo");
+-    p.waitForFinished();
+-    QString memory = p.readAllStandardOutput();
+-    p.close();
+-    bool ok = false;
+-    qlonglong output_mem = memory.toLongLong(&ok);
+-    if (ok) {
+-        totalPhysicalMemory = output_mem / 1024;
+-    }
++#elif defined(Q_OS_LINUX) || defined(Q_OS_FREEBSD)
++    long pagesize = sysconf(_SC_PAGESIZE);
++    long numpages = sysconf(_SC_PHYS_PAGES);
++
++    // Assume that page size is always a multiple of 1024, so it can be
++    // divided without losing any precision.  On the other hand, number
++    // of pages would hardly overflow `long' when multiplied by a small
++    // number (number of pages / 1024), so we should be safe here.
++    totalPhysicalMemory = (int)(numpages * (pagesize / 1024) / 1024);
+ 
+ #elif defined(Q_OS_MAC)
+ // TODO
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 00000000000..cf7d556bfcf
--- /dev/null
+++ b/biology/ugene/files/patch-src-ugeneui-src-Main.cpp
@@ -0,0 +1,20 @@
+--- src/ugeneui/src/Main.cpp.orig
++++ src/ugeneui/src/Main.cpp
+@@ -164,7 +164,7 @@ static void setDataSearchPaths() {
+         dataSearchPaths.push_back( appDirPath+RELATIVE_DEV_DATA_DIR );
+     }
+ 
+-#if (defined(Q_OS_LINUX) || defined(Q_OS_UNIX)) && defined( UGENE_DATA_DIR )
++#if defined(Q_OS_UNIX) && defined(UGENE_DATA_DIR)
+     //using directory which is set during installation process on Linux
+     QString ugene_data_dir( UGENE_DATA_DIR );
+     if( QDir(ugene_data_dir).exists() ) {
+@@ -361,7 +361,7 @@ int main(int argc, char **argv) 
+     qt_use_native_dialogs = useNative; //using local here for debugger
+ #endif
+ 
+-#if defined(Q_OS_MAC) || defined(Q_OS_LINUX)
++#if defined(Q_OS_UNIX)
+     if (envList.indexOf("UGENE_GUI_TEST=1") >= 0) {
+         QApplication::setAttribute(Qt::AA_DontUseNativeMenuBar);
+     }
diff --git a/biology/ugene/pkg-plist b/biology/ugene/pkg-plist
index 656da76b46e..9dc1c31b831 100644
--- a/biology/ugene/pkg-plist
+++ b/biology/ugene/pkg-plist
@@ -1,14 +1,48 @@
 bin/ugene
 lib/ugene/libU2Algorithm.so
+lib/ugene/libU2Algorithm.so.1
+lib/ugene/libU2Algorithm.so.1.0
+lib/ugene/libU2Algorithm.so.1.0.0
 lib/ugene/libU2Core.so
+lib/ugene/libU2Core.so.1
+lib/ugene/libU2Core.so.1.0
+lib/ugene/libU2Core.so.1.0.0
 lib/ugene/libU2Designer.so
+lib/ugene/libU2Designer.so.1
+lib/ugene/libU2Designer.so.1.0
+lib/ugene/libU2Designer.so.1.0.0
 lib/ugene/libU2Formats.so
+lib/ugene/libU2Formats.so.1
+lib/ugene/libU2Formats.so.1.0
+lib/ugene/libU2Formats.so.1.0.0
 lib/ugene/libU2Gui.so
+lib/ugene/libU2Gui.so.1
+lib/ugene/libU2Gui.so.1.0
+lib/ugene/libU2Gui.so.1.0.0
 lib/ugene/libU2Lang.so
+lib/ugene/libU2Lang.so.1
+lib/ugene/libU2Lang.so.1.0
+lib/ugene/libU2Lang.so.1.0.0
 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
+lib/ugene/libU2Script.so.1.0.0
 lib/ugene/libU2Test.so
+lib/ugene/libU2Test.so.1
+lib/ugene/libU2Test.so.1.0
+lib/ugene/libU2Test.so.1.0.0
 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
@@ -18,8 +52,17 @@ lib/ugene/libugenedb.so.1
 lib/ugene/libugenedb.so.1.0
 lib/ugene/libugenedb.so.1.0.0
 lib/ugene/plugins/libbrowser_support.so
+lib/ugene/plugins/libbrowser_support.so.1
+lib/ugene/plugins/libbrowser_support.so.1.0
+lib/ugene/plugins/libbrowser_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/libvariants.so
+lib/ugene/plugins/libvariants.so.1
+lib/ugene/plugins/libvariants.so.1.0
+lib/ugene/plugins/libvariants.so.1.0.0
 lib/ugene/plugins/linkdata_support.license
 lib/ugene/plugins/linkdata_support.plugin
 lib/ugene/plugins/variants.license
@@ -69,43 +112,161 @@ lib/ugene/plugins/hmm2.plugin
 lib/ugene/plugins/kalign.license
 lib/ugene/plugins/kalign.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
+lib/ugene/plugins/libannotator.so.1.0.0
 lib/ugene/plugins/libapi_tests.so
+lib/ugene/plugins/libapi_tests.so.1
+lib/ugene/plugins/libapi_tests.so.1.0
+lib/ugene/plugins/libapi_tests.so.1.0.0
 lib/ugene/plugins/libball.so
+lib/ugene/plugins/libball.so.1
+lib/ugene/plugins/libball.so.1.0
+lib/ugene/plugins/libball.so.1.0.0
 lib/ugene/plugins/libbiostruct3d_view.so
+lib/ugene/plugins/libbiostruct3d_view.so.1
+lib/ugene/plugins/libbiostruct3d_view.so.1.0
+lib/ugene/plugins/libbiostruct3d_view.so.1.0.0
 lib/ugene/plugins/libchroma_view.so
+lib/ugene/plugins/libchroma_view.so.1
+lib/ugene/plugins/libchroma_view.so.1.0
+lib/ugene/plugins/libchroma_view.so.1.0.0
 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/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/libdna_export.so
+lib/ugene/plugins/libdna_export.so.1
+lib/ugene/plugins/libdna_export.so.1.0
+lib/ugene/plugins/libdna_export.so.1.0.0
 lib/ugene/plugins/libdna_flexibility.so
+lib/ugene/plugins/libdna_flexibility.so.1
+lib/ugene/plugins/libdna_flexibility.so.1.0
+lib/ugene/plugins/libdna_flexibility.so.1.0.0
 lib/ugene/plugins/libdna_graphpack.so
+lib/ugene/plugins/libdna_graphpack.so.1
+lib/ugene/plugins/libdna_graphpack.so.1.0
+lib/ugene/plugins/libdna_graphpack.so.1.0.0
 lib/ugene/plugins/libdna_stat.so
+lib/ugene/plugins/libdna_stat.so.1
+lib/ugene/plugins/libdna_stat.so.1.0
+lib/ugene/plugins/libdna_stat.so.1.0.0
 lib/ugene/plugins/libdotplot.so
+lib/ugene/plugins/libdotplot.so.1
+lib/ugene/plugins/libdotplot.so.1.0
+lib/ugene/plugins/libdotplot.so.1.0.0
 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
+lib/ugene/plugins/libexternal_tool_support.so.1.0.0
 lib/ugene/plugins/libgenome_aligner.so
+lib/ugene/plugins/libgenome_aligner.so.1
+lib/ugene/plugins/libgenome_aligner.so.1.0
+lib/ugene/plugins/libgenome_aligner.so.1.0.0
 lib/ugene/plugins/libgor4.so
+lib/ugene/plugins/libgor4.so.1
+lib/ugene/plugins/libgor4.so.1.0
+lib/ugene/plugins/libgor4.so.1.0.0
 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
 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/libopencl_support.so
+lib/ugene/plugins/libopencl_support.so.1
+lib/ugene/plugins/libopencl_support.so.1.0
+lib/ugene/plugins/libopencl_support.so.1.0.0
 lib/ugene/plugins/liborf_marker.so
+lib/ugene/plugins/liborf_marker.so.1
+lib/ugene/plugins/liborf_marker.so.1.0
+lib/ugene/plugins/liborf_marker.so.1.0.0
 lib/ugene/plugins/libperf_monitor.so
+lib/ugene/plugins/libperf_monitor.so.1
+lib/ugene/plugins/libperf_monitor.so.1.0
+lib/ugene/plugins/libperf_monitor.so.1.0.0
 lib/ugene/plugins/libphylip.so
+lib/ugene/plugins/libphylip.so.1
+lib/ugene/plugins/libphylip.so.1.0
+lib/ugene/plugins/libphylip.so.1.0.0
 lib/ugene/plugins/libprimer3.so
+lib/ugene/plugins/libprimer3.so.1
+lib/ugene/plugins/libprimer3.so.1.0
+lib/ugene/plugins/libprimer3.so.1.0.0
 lib/ugene/plugins/libpsipred.so
+lib/ugene/plugins/libpsipred.so.1
+lib/ugene/plugins/libpsipred.so.1.0
+lib/ugene/plugins/libpsipred.so.1.0.0
 lib/ugene/plugins/libptools.so
+lib/ugene/plugins/libptools.so.1
+lib/ugene/plugins/libptools.so.1.0
+lib/ugene/plugins/libptools.so.1.0.0
 lib/ugene/plugins/libquery_designer.so
+lib/ugene/plugins/libquery_designer.so.1
+lib/ugene/plugins/libquery_designer.so.1.0
+lib/ugene/plugins/libquery_designer.so.1.0.0
 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
+lib/ugene/plugins/librepeat_finder.so.1.0.0
 lib/ugene/plugins/libsitecon.so
+lib/ugene/plugins/libsitecon.so.1
+lib/ugene/plugins/libsitecon.so.1.0
+lib/ugene/plugins/libsitecon.so.1.0.0
 lib/ugene/plugins/libsmith_waterman.so
+lib/ugene/plugins/libsmith_waterman.so.1
+lib/ugene/plugins/libsmith_waterman.so.1.0
+lib/ugene/plugins/libsmith_waterman.so.1.0.0
+lib/ugene/plugins/libsnp_effect.so
+lib/ugene/plugins/libsnp_effect.so.1
+lib/ugene/plugins/libsnp_effect.so.1.0
+lib/ugene/plugins/libsnp_effect.so.1.0.0
 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/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/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/opencl_support.license
 lib/ugene/plugins/opencl_support.plugin
 lib/ugene/plugins/orf_marker.license
@@ -132,6 +293,8 @@ lib/ugene/plugins/sitecon.license
 lib/ugene/plugins/sitecon.plugin
 lib/ugene/plugins/smith_waterman.license
 lib/ugene/plugins/smith_waterman.plugin
+lib/ugene/plugins/snp_effect.license
+lib/ugene/plugins/snp_effect.plugin
 lib/ugene/plugins/test_runner.license
 lib/ugene/plugins/test_runner.plugin
 %%NOX64%%lib/ugene/plugins/umuscle.license
@@ -201,6 +364,7 @@ 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/fetch-sequence.uwl
 %%DATADIR%%/cmdline/find-orfs.uwl
@@ -222,8 +386,12 @@ share/pixmaps/ugene.xpm
 %%DATADIR%%/cmdline/revcompl.uwl
 %%DATADIR%%/cmdline/sitecon-build.uwl
 %%DATADIR%%/cmdline/sitecon-search.uwl
+%%DATADIR%%/cmdline/snp.uwl
 %%DATADIR%%/enzymes/2013_08_01.bairoch.gz
 %%DATADIR%%/license
+%%PORTDOCS%%%%DOCSDIR%%/QueryDesigner_UserManual.pdf
+%%PORTDOCS%%%%DOCSDIR%%/UniproUGENE_UserManual.pdf
+%%PORTDOCS%%%%DOCSDIR%%/WorkflowDesigner_UserManual.pdf
 %%DATADIR%%/position_weight_matrix/JASPAR/all_jaspar.csv
 %%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0265.1.pfm
 %%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0266.1.pfm
@@ -973,6 +1141,8 @@ share/pixmaps/ugene.xpm
 %%DATADIR%%/query_samples/RepeatsWithORF.uql
 %%DATADIR%%/query_samples/SimpleGene.uql
 %%DATADIR%%/samples/ABIF/A01.abi
+%%DATADIR%%/samples/ACE/K26.ace
+%%DATADIR%%/samples/ACE/BL060C3.ace
 %%DATADIR%%/samples/Assembly/chrM.fa
 %%DATADIR%%/samples/Assembly/chrM.sam
 %%DATADIR%%/samples/Assembly/chrM.sorted.bam
@@ -1105,6 +1275,13 @@ share/pixmaps/ugene.xpm
 %%DATADIR%%/sitecon_models/prokaryotic/TyrR.sitecon.gz
 %%DATADIR%%/sitecon_models/prokaryotic/fis_new1.sitecon.gz
 %%DATADIR%%/sitecon_models/prokaryotic/soxS.sitecon.gz
+%%DATADIR%%/snp_scripts/SNPChIPTools.py
+%%DATADIR%%/snp_scripts/pdb_uniprot_chain_map.lst.2
+%%DATADIR%%/snp_scripts/protstability1d.py
+%%DATADIR%%/snp_scripts/protstability3d.py
+%%DATADIR%%/snp_scripts/rsnp.py
+%%DATADIR%%/snp_scripts/snp2pdbsite.py
+%%DATADIR%%/snp_scripts/update_d_db.py
 %%DATADIR%%/translations.txt
 %%DATADIR%%/weight_matrix/blosum100.txt
 %%DATADIR%%/weight_matrix/blosum30.txt
@@ -1195,7 +1372,6 @@ share/pixmaps/ugene.xpm
 %%DATADIR%%/workflow_samples/Conversions/msa2clustal.uwl
 %%DATADIR%%/workflow_samples/Conversions/query2alignment.uwl
 %%DATADIR%%/workflow_samples/Conversions/seq2gen.uwl
-%%DATADIR%%/workflow_samples/Custom elements/script-create-alignment.uwl
 %%DATADIR%%/workflow_samples/Custom elements/script-dump-sequence-info.uwl
 %%DATADIR%%/workflow_samples/Custom elements/script-linkdata-fetch-seq.uwl
 %%DATADIR%%/workflow_samples/Custom elements/script-quality-filter.uwl
@@ -1210,10 +1386,12 @@ share/pixmaps/ugene.xpm
 %%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_transcript_seq.uwl
 %%DATADIR%%/workflow_samples/NGS/tuxedo/tuxedo_main.uwl
 %%DATADIR%%/workflow_samples/NGS/tuxedo/tuxedo_main_paired.uwl
-%%DATADIR%%/workflow_samples/NGS/tuxedo/tuxedo_multiple_dataset.uwl
-%%DATADIR%%/workflow_samples/NGS/tuxedo/tuxedo_multiple_dataset_paired.uwl
+%%DATADIR%%/workflow_samples/NGS/tuxedo/tuxedo_no_novel_transcr.uwl
+%%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
@@ -1222,7 +1400,6 @@ share/pixmaps/ugene.xpm
 %%DATADIR%%/workflow_samples/Scenarios/gene_by_gene_report.uwl
 %%DATADIR%%/workflow_samples/Scenarios/merge_sequence_annotation.uwl
 %%DATADIR%%/workflow_samples/Transcriptomics/SearchTFBS.uwl
-%%DATADIR%%/workflow_samples/users/CreateAlignment.usa
 %%DATADIR%%/workflow_samples/users/Dump sequence info.usa
 %%DATADIR%%/workflow_samples/users/LinkData Fetch.usa
 %%DATADIR%%/workflow_samples/users/QualityFilter.usa
@@ -1240,6 +1417,7 @@ share/pixmaps/ugene.xpm
 @dirrm %%DATADIR%%/workflow_samples/Alignment
 @dirrm %%DATADIR%%/workflow_samples
 @dirrm %%DATADIR%%/weight_matrix
+@dirrm %%DATADIR%%/snp_scripts
 @dirrm %%DATADIR%%/sitecon_models/prokaryotic
 @dirrm %%DATADIR%%/sitecon_models/eukaryotic
 @dirrm %%DATADIR%%/sitecon_models
@@ -1259,6 +1437,7 @@ share/pixmaps/ugene.xpm
 @dirrm %%DATADIR%%/samples/EMBL
 @dirrm %%DATADIR%%/samples/CLUSTALW
 @dirrm %%DATADIR%%/samples/Assembly
+@dirrm %%DATADIR%%/samples/ACE
 @dirrm %%DATADIR%%/samples/ABIF
 @dirrm %%DATADIR%%/samples
 @dirrm %%DATADIR%%/query_samples
@@ -1276,6 +1455,7 @@ share/pixmaps/ugene.xpm
 @dirrm %%DATADIR%%/position_weight_matrix/JASPAR/fungi
 @dirrm %%DATADIR%%/position_weight_matrix/JASPAR
 @dirrm %%DATADIR%%/position_weight_matrix
+%%PORTDOCS%%@dirrm %%DOCSDIR%%
 @dirrm %%DATADIR%%/enzymes
 @dirrm %%DATADIR%%/cmdline
 @dirrm %%DATADIR%%/biostruct3d_plugin