- Update Unipro UGENE and documentation to version 1.14.0

- Remove patches integrated upstream (it's nice to have direct contact)
- Sort USES and pkg-plist, cleanup Makefile a bit while here

Approved by:	maintainer (implicit)

7 files changed, 71 insertions, 226 deletions

diff --git a/biology/ugene/Makefile b/biology/ugene/Makefile
index 75778e5fc9ab..0bde5ed60d57 100644
--- a/biology/ugene/Makefile
+++ b/biology/ugene/Makefile
@@ -2,8 +2,8 @@
 # $FreeBSD$
 
 PORTNAME=	ugene
-DISTVERSION=	1.13.1
-CATEGORIES=	biology
+DISTVERSION=	1.14.0
+CATEGORIES=	biology science
 MASTER_SITES=	http://ugene.unipro.ru/downloads/
 DISTFILES=	${DISTNAME}${EXTRACT_SUFX} QueryDesigner_UserManual.pdf \
 		UniproUGENE_UserManual.pdf WorkflowDesigner_UserManual.pdf
@@ -17,7 +17,7 @@ LICENSE=	GPLv2
 
 RUN_DEPENDS=	bash:${PORTSDIR}/shells/bash
 
-USES=		qmake execinfo
+USES=		execinfo qmake
 USE_GL=		glu
 USE_QT4=	gui webkit xml svg linguist_build moc_build qmake_build \
 		qtestlib_build rcc_build uic_build imageformats_run \
@@ -26,8 +26,8 @@ USE_XORG=	xtst
 USE_LDCONFIG=	yes
 INSTALLS_ICONS=	yes
 
-QMAKE_ARGS=	INSTALL_PREFIX=${PREFIX} UGENE_INSTALL_DATA=${DATADIR} \
-		INSTALL_MANDIR=${MAN1PREFIX}/man
+QMAKE_ARGS=	INSTALL_PREFIX="${PREFIX}" UGENE_INSTALL_DATA="${DATADIR}" \
+		INSTALL_MANDIR="${MAN1PREFIX}/man"
 ALL_TARGET=	release
 
 DOCSDIR=	${DATADIR}/manuals
@@ -42,16 +42,19 @@ DOCS_DESC=	Install official UGENE documentation (PDF)
 CXXFLAGS+=	-std=c++11
 .endif
 
-.if ${ARCH} == "amd64"
+.if ${ARCH} == amd64
 # XXX: need to manually tell the build we are on x64
 QMAKE_ARGS+=	CONFIG+=x64
-PLIST_SUB=	NOX64="@comment "
+PLIST_SUB+=	NOX64="@comment "
 .else
-PLIST_SUB=	NOX64=""
+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:
@@ -62,40 +65,14 @@ 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 '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 &,' \
-		${WRKSRC}/src/ugenecl/Makefile.Release \
-		${WRKSRC}/src/ugeneui/Makefile.Release
+	@${REINPLACE_CMD} -e '/readproc\.h/d' \
+		${WRKSRC}/src/corelibs/U2Core/src/globals/AppResources.cpp
+	@${REINPLACE_CMD} -e '1000d' \
+		${WRKSRC}/src/plugins_3rdparty/ball/src/include/BALL/DATATYPE/string.h
+	@${REINPLACE_CMD} -e 's|-bit version|& for ${OPSYS}|' \
+		${WRKSRC}/src/ugeneui/src/main_window/AboutDialogController.cpp
+.for x in ugenecl ugeneui plugins_checker
+	@${ECHO_CMD} 'LIBS += -lexecinfo' >> ${WRKSRC}/src/${x}/${x}.pro
+.endfor
 
 .include <bsd.port.post.mk>
diff --git a/biology/ugene/distinfo b/biology/ugene/distinfo
index bbc6fb51abcc..dd384463de13 100644
--- a/biology/ugene/distinfo
+++ b/biology/ugene/distinfo
@@ -1,8 +1,8 @@
-SHA256 (ugene/ugene-1.13.1.tar.gz) = 00814743de631cc144e6f01955a5183bc668684de073f600e6491b504a7760c1
-SIZE (ugene/ugene-1.13.1.tar.gz) = 19098188
-SHA256 (ugene/QueryDesigner_UserManual.pdf) = 3c5bd735c02b7ac24bd319823fde2d175b750adc1c37fe7b17e2009452a00ddd
-SIZE (ugene/QueryDesigner_UserManual.pdf) = 1306825
-SHA256 (ugene/UniproUGENE_UserManual.pdf) = 6c682c86f47a4c337eb4acdf0ae23ffa1b7fef1337d11e631655bfc943167b46
-SIZE (ugene/UniproUGENE_UserManual.pdf) = 12166178
-SHA256 (ugene/WorkflowDesigner_UserManual.pdf) = dd9a5e5860867a9a8f22d946dd94c34ee406aa648ff3d4220b0c2c5486e4bbeb
-SIZE (ugene/WorkflowDesigner_UserManual.pdf) = 8963233
+SHA256 (ugene/ugene-1.14.0.tar.gz) = e54f67d54378fcb375029267bc1ae75aec5e6e4e7c9977184be5865475ef2c42
+SIZE (ugene/ugene-1.14.0.tar.gz) = 19777919
+SHA256 (ugene/QueryDesigner_UserManual.pdf) = 2add11809ecc3225abfef417ad8d5435fed76a662081f461abb36e3d4b31cfcd
+SIZE (ugene/QueryDesigner_UserManual.pdf) = 824781
+SHA256 (ugene/UniproUGENE_UserManual.pdf) = c4aa20246988978c6b40a06f7753f78d204ee3155cb8876a3d665b9ebf5641db
+SIZE (ugene/UniproUGENE_UserManual.pdf) = 12263913
+SHA256 (ugene/WorkflowDesigner_UserManual.pdf) = 9dc5b25bdc8d7af1473f5a860debebfd238bfef018cc7a9d69816354efcfa202
+SIZE (ugene/WorkflowDesigner_UserManual.pdf) = 8639016
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
deleted file mode 100644
index bfbfccd0be52..000000000000
--- a/biology/ugene/files/patch-src-corelibs-U2Core-src-globals-AppResources.cpp
+++ /dev/null
@@ -1,73 +0,0 @@
---- 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_WIN
-     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
deleted file mode 100644
index 86be6655da16..000000000000
--- a/biology/ugene/files/patch-src-shtirlitz-Shtirlitz.cpp
+++ /dev/null
@@ -1,14 +0,0 @@
---- 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
deleted file mode 100644
index 7f75a92202e3..000000000000
--- a/biology/ugene/files/patch-src-ugenem-src-SendReportDialog.cpp
+++ /dev/null
@@ -1,49 +0,0 @@
---- 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
deleted file mode 100644
index cf7d556bfcf7..000000000000
--- a/biology/ugene/files/patch-src-ugeneui-src-Main.cpp
+++ /dev/null
@@ -1,20 +0,0 @@
---- 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 9dc1c31b8314..f1822c8a7201 100644
--- a/biology/ugene/pkg-plist
+++ b/biology/ugene/pkg-plist
@@ -51,36 +51,20 @@ 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/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
-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
 lib/ugene/plugins/ball.plugin
 lib/ugene/plugins/biostruct3d_view.license
 lib/ugene/plugins/biostruct3d_view.plugin
+lib/ugene/plugins/browser_support.license
+lib/ugene/plugins/browser_support.plugin
 lib/ugene/plugins/chroma_view.license
 lib/ugene/plugins/chroma_view.plugin
 lib/ugene/plugins/circular_view.license
@@ -109,6 +93,8 @@ 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/libCoreTests.so
@@ -135,6 +121,10 @@ 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/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/libchroma_view.so
 lib/ugene/plugins/libchroma_view.so.1
 lib/ugene/plugins/libchroma_view.so.1.0
@@ -191,10 +181,18 @@ 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/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/libopencl_support.so
 lib/ugene/plugins/libopencl_support.so.1
 lib/ugene/plugins/libopencl_support.so.1.0
@@ -259,6 +257,10 @@ lib/ugene/plugins/libtest_runner.so.1.0.0
 %%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/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/libweight_matrix.so
 lib/ugene/plugins/libweight_matrix.so.1
 lib/ugene/plugins/libweight_matrix.so.1.0
@@ -267,6 +269,8 @@ 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/opencl_support.license
 lib/ugene/plugins/opencl_support.plugin
 lib/ugene/plugins/orf_marker.license
@@ -299,10 +303,13 @@ 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/variants.license
+lib/ugene/plugins/variants.plugin
 lib/ugene/plugins/weight_matrix.license
 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
@@ -366,6 +373,7 @@ share/pixmaps/ugene.xpm
 %%DATADIR%%/cmdline/convert-seq.uwl
 %%DATADIR%%/cmdline/das_annotation.uwl
 %%DATADIR%%/cmdline/extract-sequence.uwl
+%%DATADIR%%/cmdline/extract_consensus.uwl
 %%DATADIR%%/cmdline/fetch-sequence.uwl
 %%DATADIR%%/cmdline/find-orfs.uwl
 %%DATADIR%%/cmdline/find-repeats.uwl
@@ -387,7 +395,16 @@ share/pixmaps/ugene.xpm
 %%DATADIR%%/cmdline/sitecon-build.uwl
 %%DATADIR%%/cmdline/sitecon-search.uwl
 %%DATADIR%%/cmdline/snp.uwl
+%%DATADIR%%/custom_annotations/plasmid_features.txt
 %%DATADIR%%/enzymes/2013_08_01.bairoch.gz
+%%DATADIR%%/genome_lengths/danRer7.genome
+%%DATADIR%%/genome_lengths/ecoli.genome
+%%DATADIR%%/genome_lengths/hg18.genome
+%%DATADIR%%/genome_lengths/hg19.genome
+%%DATADIR%%/genome_lengths/mm10.genome
+%%DATADIR%%/genome_lengths/mm8.genome
+%%DATADIR%%/genome_lengths/mm9.genome
+%%DATADIR%%/genome_lengths/test.genome
 %%DATADIR%%/license
 %%PORTDOCS%%%%DOCSDIR%%/QueryDesigner_UserManual.pdf
 %%PORTDOCS%%%%DOCSDIR%%/UniproUGENE_UserManual.pdf
@@ -1141,8 +1158,8 @@ 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/ACE/K26.ace
 %%DATADIR%%/samples/Assembly/chrM.fa
 %%DATADIR%%/samples/Assembly/chrM.sam
 %%DATADIR%%/samples/Assembly/chrM.sorted.bam
@@ -1372,6 +1389,8 @@ 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/casava-fastq-filter.uwl
+%%DATADIR%%/workflow_samples/Custom elements/fastq-trimmer.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
@@ -1395,12 +1414,15 @@ share/pixmaps/ugene.xpm
 %%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/extract_consensus.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/CASAVA FASTQ filter.usa
 %%DATADIR%%/workflow_samples/users/Dump sequence info.usa
+%%DATADIR%%/workflow_samples/users/FASTQ Trimmer.usa
 %%DATADIR%%/workflow_samples/users/LinkData Fetch.usa
 %%DATADIR%%/workflow_samples/users/QualityFilter.usa
 @dirrm %%DATADIR%%/workflow_samples/users
@@ -1456,7 +1478,9 @@ share/pixmaps/ugene.xpm
 @dirrm %%DATADIR%%/position_weight_matrix/JASPAR
 @dirrm %%DATADIR%%/position_weight_matrix
 %%PORTDOCS%%@dirrm %%DOCSDIR%%
+@dirrm %%DATADIR%%/genome_lengths
 @dirrm %%DATADIR%%/enzymes
+@dirrm %%DATADIR%%/custom_annotations
 @dirrm %%DATADIR%%/cmdline
 @dirrm %%DATADIR%%/biostruct3d_plugin
 @dirrm %%DATADIR%%/back_translation/Yeast