8 files changed, 325 insertions, 79 deletions

diff --git a/biology/ugene/Makefile b/biology/ugene/Makefile
index 324afd10c12a..e1a7817c020f 100644
--- a/biology/ugene/Makefile
+++ b/biology/ugene/Makefile
@@ -2,7 +2,7 @@
 # $FreeBSD$
 
 PORTNAME=	ugene
-DISTVERSION=	1.11.4
+DISTVERSION=	1.12.3
 CATEGORIES=	biology
 MASTER_SITES=	http://ugene.unipro.ru/downloads/
 
@@ -11,41 +11,54 @@ COMMENT=	Free, open-source, cross-platform bioinformatics toolkit
 
 LICENSE=	GPLv2
 
-LIB_DEPENDS=	execinfo:${PORTSDIR}/devel/libexecinfo
+.if !exists(/usr/include/execinfo.h)
+LIB_DEPENDS=	libexecinfo.so:${PORTSDIR}/devel/libexecinfo
+.endif
 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
 USE_XORG=	xtst
-
 USE_LDCONFIG=	yes
 INSTALLS_ICONS=	yes
 
-MAN1=		${PORTNAME}.1
-MANCOMPRESSED=	yes
+QMAKE_ARGS=	INSTALL_PREFIX=${PREFIX} UGENE_INSTALL_DATA=${DATADIR} \
+		INSTALL_MANDIR=${MAN1PREFIX}/man
+ALL_TARGET=	release
 
-NO_STAGE=	yes
 .include <bsd.port.pre.mk>
 
+.if ${OSVERSION} > 1000054
+CXXFLAGS+=	-std=c++11
+.endif
+
 .if ${ARCH} == "amd64"
-# need to manually tell the build we are on x64
-CARCH=		CONFIG+=x64
+# XXX: need to manually tell the build we are on x64
+QMAKE_ARGS+=	CONFIG+=x64
 PLIST_SUB=	NOX64="@comment "
 .else
 PLIST_SUB=	NOX64=""
 .endif
 
-# yes, bash is required, stuff will not execute with sh
+.if ${MACHINE_CPU:Msse2}
+QMAKE_ARGS+=	UGENE_SSE2_DETECTED=1
+.endif
+
 post-patch:
+# yes, bash is required, stuff will not execute with sh
 	@${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
 
-do-configure:
-	@cd ${CONFIGURE_WRKSRC} && ${SETENV} ${CONFIGURE_ENV} ${QMAKE} \
-		PREFIX=${PREFIX} INSTALL_PREFIX=${PREFIX} \
-		INSTALL_MANDIR=${MAN1PREFIX}/man ${CARCH} \
-		UGENE_INSTALL_DATA=${DATADIR} -r ${PORTNAME}.pro
+post-configure:
+	@${REINPLACE_CMD} -e '/^LFLAGS/s,-pthread,-lexecinfo &,' \
+		${WRKSRC}/src/ugenecl/Makefile.Release \
+		${WRKSRC}/src/ugeneui/Makefile.Release
 
 .include <bsd.port.post.mk>
diff --git a/biology/ugene/distinfo b/biology/ugene/distinfo
index 23b6433eef20..bad5b97da265 100644
--- a/biology/ugene/distinfo
+++ b/biology/ugene/distinfo
@@ -1,2 +1,2 @@
-SHA256 (ugene-1.11.4.tar.gz) = 5b9b914e7ef5a3d3658f3346cccdb5cd6583b03db3b7bed7e163cb5cfd5663fa
-SIZE (ugene-1.11.4.tar.gz) = 14761290
+SHA256 (ugene-1.12.3.tar.gz) = 6642ec6ef5110b50b38c9620be4a98101d9a7b325a61a202ee7e0f2c67d45496
+SIZE (ugene-1.12.3.tar.gz) = 17611949
diff --git a/biology/ugene/files/patch-clang-fixes b/biology/ugene/files/patch-clang-fixes
new file mode 100644
index 000000000000..3abf7b57fed1
--- /dev/null
+++ b/biology/ugene/files/patch-clang-fixes
@@ -0,0 +1,91 @@
+--- 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
new file mode 100644
index 000000000000..655f6c86d153
--- /dev/null
+++ b/biology/ugene/files/patch-gtest-std::tr1::tuple-fix
@@ -0,0 +1,34 @@
+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-U2Private-src-CrashHandler.cpp b/biology/ugene/files/patch-src-corelibs-U2Private-src-CrashHandler.cpp
deleted file mode 100644
index 1e5e161bac43..000000000000
--- a/biology/ugene/files/patch-src-corelibs-U2Private-src-CrashHandler.cpp
+++ /dev/null
@@ -1,20 +0,0 @@
---- ./src/corelibs/U2Private/src/CrashHandler.cpp.orig	2012-10-30 15:36:22.000000000 +0100
-+++ ./src/corelibs/U2Private/src/CrashHandler.cpp	2012-10-30 15:47:47.000000000 +0100
-@@ -253,7 +253,7 @@
-     }
-     //handler = AddVectoredExceptionHandler(1, CrashHandlerFunc);
-     
--#elif defined( Q_OS_MAC)
-+#elif defined( Q_OS_MAC ) || defined ( Q_OS_FREEBSD )
-     return; //TODO: implement crash hander for MAC OS
- #else
-     stack_t sigstk;
-@@ -284,7 +284,7 @@
- void CrashHandler::runMonitorProcess(const QString &exceptionType) {
-     QString path = QCoreApplication::applicationDirPath() + "/ugenem";
- 
--#ifndef Q_OS_WIN
-+#if !defined ( Q_OS_WIN ) && !defined ( Q_OS_FREEBSD )
-     char pid_buf[30];
-     sprintf(pid_buf, "%d", getpid());
-     char name_buf[512];
diff --git a/biology/ugene/files/patch-src-plugins_3rdparty-umuscle-src-muscle-intmath.cpp b/biology/ugene/files/patch-src-plugins_3rdparty-umuscle-src-muscle-intmath.cpp
deleted file mode 100644
index f9f6d167af29..000000000000
--- a/biology/ugene/files/patch-src-plugins_3rdparty-umuscle-src-muscle-intmath.cpp
+++ /dev/null
@@ -1,30 +0,0 @@
---- ./src/plugins_3rdparty/umuscle/src/muscle/intmath.cpp.orig	2012-12-26 17:43:44.000000000 +0800
-+++ ./src/plugins_3rdparty/umuscle/src/muscle/intmath.cpp	2013-02-25 17:25:06.000000000 +0800
-@@ -9,13 +9,6 @@
- 	return (PROB) pow(2.0, (double) Score/INTSCALE);
- 	}
- 
--static const double log2e = log2(exp(1.0));
--
--double lnTolog2(double ln)
--	{
--	return ln*log2e;
--	}
--
- double log2(double x)
- 	{
- 	if (0 == x)
-@@ -27,6 +20,13 @@
- 	return log(x)*dInvLn2;
- 	}
- 
-+static const double log2e = log2(exp(1.0));
-+
-+double lnTolog2(double ln)
-+	{
-+	return ln*log2e;
-+	}
-+
- SCORE ProbToScore(PROB Prob)
- 	{
- 	if (0.0 == Prob)
diff --git a/biology/ugene/pkg-descr b/biology/ugene/pkg-descr
index 9ac1f2d9ce6d..a5e84919dfc2 100644
--- a/biology/ugene/pkg-descr
+++ b/biology/ugene/pkg-descr
@@ -1,12 +1,12 @@
-Unipro UGENE is a multiplatform open-source software with the main goal of
+Unipro UGENE is multiplatform, open-source software with the main goal of
 assisting molecular biologists without much expertise in bioinformatics to
-manage, analyze and visualize their data.  UGENE integrates widely used
-bioinformatics tools within a common user interface.
+manage, analyze, and visualize their data.  UGENE integrates widely used
+bioinformatics tools within one common user interface.
 
-The toolkit supports multiple biological data formats and allows the
+UGENE toolkit supports multiple biological data formats and allows the
 retrieval of data from remote data sources.  It provides visualization
 modules for biological objects such as annotated genome sequences, Next
 Generation Sequencing (NGS) assembly data, multiple sequence alignments,
-phylogenetic trees and 3D structures.
+phylogenetic trees, and 3D structures.
 
 WWW: http://ugene.unipro.ru/
diff --git a/biology/ugene/pkg-plist b/biology/ugene/pkg-plist
index 39415697299c..e0f4ae7a6206 100644
--- a/biology/ugene/pkg-plist
+++ b/biology/ugene/pkg-plist
@@ -10,13 +10,28 @@ lib/ugene/libU2Remote.so
 lib/ugene/libU2Test.so
 lib/ugene/libU2View.so
 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/libbrowser_support.so
+lib/ugene/plugins/liblinkdata_support.so
+lib/ugene/plugins/libvariants.so
+lib/ugene/plugins/linkdata_support.license
+lib/ugene/plugins/linkdata_support.plugin
+lib/ugene/plugins/variants.license
+lib/ugene/plugins/variants.plugin
 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/browser_support.license
+lib/ugene/plugins/browser_support.plugin
 lib/ugene/plugins/api_tests.license
 lib/ugene/plugins/api_tests.plugin
 lib/ugene/plugins/ball.license
@@ -133,6 +148,7 @@ lib/ugene/ugene
 lib/ugene/ugenecl
 lib/ugene/ugenem
 lib/ugene/ugeneui
+man/man1/ugene.1.gz
 share/applications/ugene.desktop
 share/pixmaps/ugene.png
 share/pixmaps/ugene.xpm
@@ -177,21 +193,20 @@ share/pixmaps/ugene.xpm
 %%DATADIR%%/back_translation/Yeast/Saccharomyces_cerevisiae_(baker's_yeast).cut
 %%DATADIR%%/back_translation/tables.xml
 %%DATADIR%%/biostruct3d_plugin/BioStruct3DLinks.txt
+%%DATADIR%%/cmdline/align-clustalo.uwl
 %%DATADIR%%/cmdline/align-clustalw.uwl
 %%DATADIR%%/cmdline/align-kalign.uwl
 %%DATADIR%%/cmdline/align-mafft.uwl
 %%DATADIR%%/cmdline/align-tcoffee.uwl
 %%DATADIR%%/cmdline/align.uwl
-%%DATADIR%%/cmdline/bowtie-build.uwl
-%%DATADIR%%/cmdline/bowtie.uwl
 %%DATADIR%%/cmdline/convert-msa.uwl
 %%DATADIR%%/cmdline/convert-seq.uwl
 %%DATADIR%%/cmdline/extract-sequence.uwl
 %%DATADIR%%/cmdline/fetch-sequence.uwl
-%%DATADIR%%/cmdline/fetch.uwl
 %%DATADIR%%/cmdline/find-orfs.uwl
 %%DATADIR%%/cmdline/find-repeats.uwl
 %%DATADIR%%/cmdline/find-sw.uwl
+%%DATADIR%%/cmdline/gene-by-gene.uwl
 %%DATADIR%%/cmdline/generate-dna.uwl
 %%DATADIR%%/cmdline/hmm2-build.uwl
 %%DATADIR%%/cmdline/hmm2-search.uwl
@@ -207,8 +222,7 @@ share/pixmaps/ugene.xpm
 %%DATADIR%%/cmdline/revcompl.uwl
 %%DATADIR%%/cmdline/sitecon-build.uwl
 %%DATADIR%%/cmdline/sitecon-search.uwl
-%%DATADIR%%/enzymes/rebase_v003_all.bairoch.gz
-%%DATADIR%%/enzymes/rebase_v003_t2_com.bairoch.gz
+%%DATADIR%%/enzymes/2013_08_01.bairoch.gz
 %%DATADIR%%/license
 %%DATADIR%%/position_weight_matrix/JASPAR/all_jaspar.csv
 %%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0265.1.pfm
@@ -389,6 +403,131 @@ share/pixmaps/ugene.xpm
 %%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0440.1.pfm
 %%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0441.1.pfm
 %%DATADIR%%/position_weight_matrix/JASPAR/fungi/matrix_list.txt
+%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0010.1.pfm
+%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0011.1.pfm
+%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0012.1.pfm
+%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0013.1.pfm
+%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0015.1.pfm
+%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0016.1.pfm
+%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0022.1.pfm
+%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0023.1.pfm
+%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0026.1.pfm
+%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA00445.1.pfm
+%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0049.1.pfm
+%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0085.1.pfm
+%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0086.1.pfm
+%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0094.2.pfm
+%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0126.1.pfm
+%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0165.1.pfm
+%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0166.1.pfm
+%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0167.1.pfm
+%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0168.1.pfm
+%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0169.1.pfm
+%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0170.1.pfm
+%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0171.1.pfm
+%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0172.1.pfm
+%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0173.1.pfm
+%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0174.1.pfm
+%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0175.1.pfm
+%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0176.1.pfm
+%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0177.1.pfm
+%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0178.1.pfm
+%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0179.1.pfm
+%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0180.1.pfm
+%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0181.1.pfm
+%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0182.1.pfm
+%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0183.1.pfm
+%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0184.1.pfm
+%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0185.1.pfm
+%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0186.1.pfm
+%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0187.1.pfm
+%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0188.1.pfm
+%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0189.1.pfm
+%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0190.1.pfm
+%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0191.1.pfm
+%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0192.1.pfm
+%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0193.1.pfm
+%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0194.1.pfm
+%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0195.1.pfm
+%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0196.1.pfm
+%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0197.1.pfm
+%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0198.1.pfm
+%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0199.1.pfm
+%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0200.1.pfm
+%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0201.1.pfm
+%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0202.1.pfm
+%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0203.1.pfm
+%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0204.1.pfm
+%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0205.1.pfm
+%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0206.1.pfm
+%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0207.1.pfm
+%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0208.1.pfm
+%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0209.1.pfm
+%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0210.1.pfm
+%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0211.1.pfm
+%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0212.1.pfm
+%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0213.1.pfm
+%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0214.1.pfm
+%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0215.1.pfm
+%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0216.1.pfm
+%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0217.1.pfm
+%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0218.1.pfm
+%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0219.1.pfm
+%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0220.1.pfm
+%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0221.1.pfm
+%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0222.1.pfm
+%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0223.1.pfm
+%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0224.1.pfm
+%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0225.1.pfm
+%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0226.1.pfm
+%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0227.1.pfm
+%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0228.1.pfm
+%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0229.1.pfm
+%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0230.1.pfm
+%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0231.1.pfm
+%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0232.1.pfm
+%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0233.1.pfm
+%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0234.1.pfm
+%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0235.1.pfm
+%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0236.1.pfm
+%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0237.1.pfm
+%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0238.1.pfm
+%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0239.1.pfm
+%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0240.1.pfm
+%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0241.1.pfm
+%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0242.1.pfm
+%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0243.1.pfm
+%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0244.1.pfm
+%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0245.1.pfm
+%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0246.1.pfm
+%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0247.1.pfm
+%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0248.1.pfm
+%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0249.1.pfm
+%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0250.1.pfm
+%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0251.1.pfm
+%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0252.1.pfm
+%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0253.1.pfm
+%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0254.1.pfm
+%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0255.1.pfm
+%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0256.1.pfm
+%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0257.1.pfm
+%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0443.1.pfm
+%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0444.1.pfm
+%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0446.1.pfm
+%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0447.1.pfm
+%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0448.1.pfm
+%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0449.1.pfm
+%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0450.1.pfm
+%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0451.1.pfm
+%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0452.1.pfm
+%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0453.1.pfm
+%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0454.1.pfm
+%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0455.1.pfm
+%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0456.1.pfm
+%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0457.1.pfm
+%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0458.1.pfm
+%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0459.1.pfm
+%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0460.1.pfm
 %%DATADIR%%/position_weight_matrix/JASPAR/insects/matrix_list.txt
 %%DATADIR%%/position_weight_matrix/JASPAR/nematodes/MA0260.1.pfm
 %%DATADIR%%/position_weight_matrix/JASPAR/nematodes/MA0261.1.pfm
@@ -834,8 +973,6 @@ share/pixmaps/ugene.xpm
 %%DATADIR%%/query_samples/RepeatsWithORF.uql
 %%DATADIR%%/query_samples/SimpleGene.uql
 %%DATADIR%%/samples/ABIF/A01.abi
-%%DATADIR%%/samples/ACE/BL060C3.ace
-%%DATADIR%%/samples/ACE/K26.ace
 %%DATADIR%%/samples/Assembly/chrM.fa
 %%DATADIR%%/samples/Assembly/chrM.sam
 %%DATADIR%%/samples/Assembly/chrM.sorted.bam
@@ -1058,7 +1195,9 @@ 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
 %%DATADIR%%/workflow_samples/Data marking/annotation_marker.uwl
 %%DATADIR%%/workflow_samples/Data marking/length_marker.uwl
@@ -1067,12 +1206,32 @@ 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/call_variants.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/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_single_dataset.uwl
+%%DATADIR%%/workflow_samples/NGS/tuxedo/tuxedo_single_dataset_paired.uwl
+%%DATADIR%%/workflow_samples/NGS/tuxedo.uwl
+%%DATADIR%%/workflow_samples/Scenarios/filter_matched.uwl
+%%DATADIR%%/workflow_samples/Scenarios/find_sequences.uwl
+%%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
 @dirrm %%DATADIR%%/workflow_samples/users
 @dirrm %%DATADIR%%/workflow_samples/Transcriptomics
+@dirrm %%DATADIR%%/workflow_samples/Scenarios
+@dirrm %%DATADIR%%/workflow_samples/NGS/tuxedo
+@dirrm %%DATADIR%%/workflow_samples/NGS/cistrome
+@dirrm %%DATADIR%%/workflow_samples/NGS
 @dirrm %%DATADIR%%/workflow_samples/HMMER
 @dirrm %%DATADIR%%/workflow_samples/Data merging
 @dirrm %%DATADIR%%/workflow_samples/Data marking
@@ -1100,7 +1259,6 @@ 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