Attachment #196793 for bug #229463

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# $FreeBSD$

PORTNAME=	ugene
DISTVERSION=	1.31.0
PORTREVISION=	3
CATEGORIES=	biology science
MASTER_SITES=	http://ugene.unipro.ru/downloads/
DISTFILES=	${DISTNAME}${EXTRACT_SUFX} QueryDesigner_UserManual.pdf \

MAINTAINER=	h2+fbsdports@fsfe.org
COMMENT=	Free, open-source, cross-platform bioinformatics toolkit

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 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 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:

		${WRKSRC}/installer/_common_data/ugene
	@${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 \

Lines 1-5 Link Here

(-)biology/ugene/distinfo (-2 / +3 lines)
1	SHA256 (ugene/ugene-1.22.0.tar.gz) = ee46be799c9f02a9b6a89f13747a4918d5c96c01676dc2d4cc4a4c98278912b6	1	TIMESTAMP = 1535840965
2	SIZE (ugene/ugene-1.22.0.tar.gz) = 20986853	2	SHA256 (ugene/ugene-1.31.0.tar.gz) = d1f46306834a292618cc54b31060b69da5b0b18da311a55bf82ab42f5a434320
		3	SIZE (ugene/ugene-1.31.0.tar.gz) = 20656562
3	SHA256 (ugene/QueryDesigner_UserManual.pdf) = 5d232c0de7e9d1fd32b8ee0a78f9f4abe1ab9d6536ec3958c47de29f3096faf4	4	SHA256 (ugene/QueryDesigner_UserManual.pdf) = 5d232c0de7e9d1fd32b8ee0a78f9f4abe1ab9d6536ec3958c47de29f3096faf4
4	SIZE (ugene/QueryDesigner_UserManual.pdf) = 855662	5	SIZE (ugene/QueryDesigner_UserManual.pdf) = 855662
5	SHA256 (ugene/UniproUGENE_UserManual.pdf) = ae6aef32a6e92a30ba7c36cdd894a8caf634d678f15da7ad9eab52b6f40b9ed6	6	SHA256 (ugene/UniproUGENE_UserManual.pdf) = ae6aef32a6e92a30ba7c36cdd894a8caf634d678f15da7ad9eab52b6f40b9ed6




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>




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"




--- 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 \

 
 SOURCES += src/AppContextImpl.cpp \
            src/AppSettingsImpl.cpp \
@@ -30,23 +25,13 @@ SOURCES += src/AppContextImpl.cpp \
            src/PluginSupportImpl.cpp \
            src/ServiceRegistryImpl.cpp \
            src/SettingsImpl.cpp \

-           src/crash_handler/StackWalker.cpp
+           src/TaskSchedulerImpl.cpp
 
 TRANSLATIONS += transl/russian.ts
 
 win32 {
     HEADERS += src/crash_handler/CrashHandlerPrivateWin.h
     SOURCES += src/crash_handler/CrashHandlerPrivateWin.cpp
-    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
-}




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"
 




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);

Lines 1-11 Link Here

(-)biology/ugene/files/patch-src_libs__3rdparty_samtools_samtools.pri (-11 lines)
1	--- src/libs_3rdparty/samtools/samtools.pri.orig 2016-03-31 12:21:56 UTC
2	+++ src/libs_3rdparty/samtools/samtools.pri
3	@@ -3,7 +3,7 @@ UGENE_RELATIVE_DESTDIR = ''
4
5	TEMPLATE = lib
6	CONFIG +=thread debug_and_release staticlib warn_off
7	-INCLUDEPATH += src src/samtools ../../include /usr/include
8	+INCLUDEPATH += src src/samtools ../../include
9	win32 : INCLUDEPATH += src/samtools/win32
10	DEFINES+="_FILE_OFFSET_BITS=64" _LARGEFILE64_SOURCE _USE_KNETFILE
11	win32 : DEFINES += _USE_MATH_DEFINES "inline=__inline" "__func__=__FUNCTION__" "R_OK=4" "atoll=_atoi64" "alloca=_alloca"

Lines 1-10 Link Here

(-)biology/ugene/files/patch-src_plugins__3rdparty_phylip_src_phylip.h (-10 lines)
1	--- src/plugins_3rdparty/phylip/src/phylip.h.orig 2017-12-30 19:54:56 UTC
2	+++ src/plugins_3rdparty/phylip/src/phylip.h
3	@@ -271,7 +271,6 @@ MALLOCRETURN *mymalloc(long);
4	#define MAXNCH 30 /* must be greater than or equal to nmlngth */
5	#define maxcategs 9 /* maximum number of site types */
6	#define maxcategs2 11 /* maximum number of site types + 2 */
7	-#define point "."
8	#define pointe '.'
9	#define down 2
10	#define MAXSHIMOTREES 100




--- 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() {

Lines 1-11 Link Here

(-)biology/ugene/files/patch-src_plugins__3rdparty_variants_variants.pri (-11 lines)
1	--- src/plugins_3rdparty/variants/variants.pri.orig 2016-03-31 12:22:09 UTC
2	+++ src/plugins_3rdparty/variants/variants.pri
3	@@ -20,7 +20,7 @@ use_bundled_zlib() {
4	win32 : LIBS += -lwsock32
5
6
7	-INCLUDEPATH += src ../../include /usr/include
8	+INCLUDEPATH += src ../../include
9	INCLUDEPATH += ../../libs_3rdparty/samtools/src/samtools
10	INCLUDEPATH += ../../libs_3rdparty/samtools/src
11	INCLUDEPATH += ../../libs_3rdparty/samtools/src/samtools/bcftools

Lines 1-4 Link Here

(-)biology/ugene/files/patch-src_plugins__checker_src_Main.cpp (-2 / +2 lines)
1	--- src/plugins_checker/src/Main.cpp.orig 2016-03-31 12:22:09 UTC	1	--- src/plugins_checker/src/Main.cpp.orig 2018-08-16 13:59:06 UTC
2	+++ src/plugins_checker/src/Main.cpp	2	+++ src/plugins_checker/src/Main.cpp
3	@@ -39,7 +39,7 @@	3	@@ -39,7 +39,7 @@
4	#include <ServiceRegistryImpl.h>	4	#include <ServiceRegistryImpl.h>
Lines 20-26 Link Here
20		20
21	const char* build = QT_VERSION_STR, *runtime = qVersion();	21	const char* build = QT_VERSION_STR, *runtime = qVersion();
22	if (strcmp(build, runtime) > 0){	22	if (strcmp(build, runtime) > 0){
23	@@ -140,7 +142,7 @@ int main(int argc, char **argv)	23	@@ -141,7 +143,7 @@ int main(int argc, char **argv)
24	delete cmdLineRegistry;	24	delete cmdLineRegistry;
25	appContext->setCMDLineRegistry(NULL);	25	appContext->setCMDLineRegistry(NULL);
26		26




--- 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

Lines 1-6 Link Here

(-)biology/ugene/files/patch-src_ugenecl_src_Main.cpp (-4 / +8 lines)
1	--- src/ugenecl/src/Main.cpp.orig 2016-03-31 12:22:19 UTC	1	--- src/ugenecl/src/Main.cpp.orig 2018-08-16 13:59:20 UTC
2	+++ src/ugenecl/src/Main.cpp	2	+++ src/ugenecl/src/Main.cpp
3	@@ -94,7 +94,7 @@	3	@@ -93,7 +93,7 @@
4	#include <ServiceRegistryImpl.h>	4	#include <ServiceRegistryImpl.h>
5	#include <SettingsImpl.h>	5	#include <SettingsImpl.h>
6	#include <TaskSchedulerImpl.h>	6	#include <TaskSchedulerImpl.h>
Lines 9-15 Link Here
9		9
10	// local project imports	10	// local project imports
11	#include "DumpHelpTask.h"	11	#include "DumpHelpTask.h"
12	@@ -192,9 +192,11 @@ static void setSearchPaths() {	12	@@ -191,6 +191,7 @@ static void setSearchPaths() {
13		13
14	int main(int argc, char **argv)	14	int main(int argc, char **argv)
15	{	15	{
Lines 17-26 Link Here
17	if (CrashHandler::isEnabled()) {	17	if (CrashHandler::isEnabled()) {
18	CrashHandler::setupHandler();	18	CrashHandler::setupHandler();
19	}	19	}
		20	@@ -198,6 +199,7 @@ int main(int argc, char **argv)
		21	if (qgetenv(ENV_SEND_CRASH_REPORTS) == "0") {
		22	CrashHandler::setSendCrashReports(false);
		23	}
20	+#endif	24	+#endif
		25
21	const char* build = QT_VERSION_STR, *runtime = qVersion();	26	const char* build = QT_VERSION_STR, *runtime = qVersion();
22	if (strcmp(build, runtime) > 0){	27	if (strcmp(build, runtime) > 0){
23	printf("Installed Qt version must be %s or greater \r\n", QT_VERSION_STR);
24	@@ -617,7 +619,7 @@ int main(int argc, char **argv)	28	@@ -617,7 +619,7 @@ int main(int argc, char **argv)
25	delete pwr;	29	delete pwr;
26	appContext->setAlignmentAlgorithmsRegistry(NULL);	30	appContext->setAlignmentAlgorithmsRegistry(NULL);

Lines 1-6 Link Here

(-)biology/ugene/files/patch-src_ugeneui_src_Main.cpp (-4 / +8 lines)
1	--- src/ugeneui/src/Main.cpp.orig 2016-03-31 12:22:18 UTC	1	--- src/ugeneui/src/Main.cpp.orig 2018-08-16 13:59:19 UTC
2	+++ src/ugeneui/src/Main.cpp	2	+++ src/ugeneui/src/Main.cpp
3	@@ -134,7 +134,7 @@	3	@@ -136,7 +136,7 @@
4	#include <ServiceRegistryImpl.h>	4	#include <ServiceRegistryImpl.h>
5	#include <SettingsImpl.h>	5	#include <SettingsImpl.h>
6	#include <TaskSchedulerImpl.h>	6	#include <TaskSchedulerImpl.h>
Lines 9-15 Link Here
9		9
10	#include "app_settings/AppSettingsGUIImpl.h"	10	#include "app_settings/AppSettingsGUIImpl.h"
11	#include "app_settings/logview_settings/LogSettingsGUIController.h"	11	#include "app_settings/logview_settings/LogSettingsGUIController.h"
12	@@ -343,9 +343,11 @@ void fixMacFonts() {	12	@@ -353,6 +353,7 @@ void fixMacFonts() {
13		13
14	int main(int argc, char **argv)	14	int main(int argc, char **argv)
15	{	15	{
Lines 17-27 Link Here
17	if (CrashHandler::isEnabled()) {	17	if (CrashHandler::isEnabled()) {
18	CrashHandler::setupHandler();	18	CrashHandler::setupHandler();
19	}	19	}
		20	@@ -360,6 +361,7 @@ int main(int argc, char **argv)
		21	if (qgetenv(ENV_SEND_CRASH_REPORTS) == "0") {
		22	CrashHandler::setSendCrashReports(false);
		23	}
20	+#endif	24	+#endif
21		25
22	QT_REQUIRE_VERSION( argc, argv, QT_VERSION_STR );	26	QT_REQUIRE_VERSION( argc, argv, QT_VERSION_STR );
23		27
24	@@ -966,7 +968,7 @@ int main(int argc, char **argv)	28	@@ -973,7 +975,7 @@ int main(int argc, char **argv)
25	}	29	}
26		30
27	UgeneUpdater::onClose();	31	UgeneUpdater::onClose();




--- ugene.pro.orig	2018-08-16 13:58:51 UTC
+++ ugene.pro
@@ -20,7 +20,6 @@ use_bundled_zlib() {
 }

-          src/libs_3rdparty/breakpad \
           src/libs_3rdparty/qscore \
           src/libs_3rdparty/sqlite3 \
           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 =
-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

Lines 1-4 Link Here

(-)biology/ugene/pkg-plist (-35 / +80 lines)
1	bin/ugene	1	bin/ugene
		2	lib/ugene/libQSpec.so
		3	lib/ugene/libQSpec.so.1
		4	lib/ugene/libQSpec.so.1.0
		5	lib/ugene/libQSpec.so.1.0.0
2	lib/ugene/libU2Algorithm.so	6	lib/ugene/libU2Algorithm.so
3	lib/ugene/libU2Algorithm.so.1	7	lib/ugene/libU2Algorithm.so.1
4	lib/ugene/libU2Algorithm.so.1.0	8	lib/ugene/libU2Algorithm.so.1.0
Lines 27-36 Link Here
27	lib/ugene/libU2Private.so.1	31	lib/ugene/libU2Private.so.1
28	lib/ugene/libU2Private.so.1.0	32	lib/ugene/libU2Private.so.1.0
29	lib/ugene/libU2Private.so.1.0.0	33	lib/ugene/libU2Private.so.1.0.0
30	lib/ugene/libU2Remote.so
31	lib/ugene/libU2Remote.so.1
32	lib/ugene/libU2Remote.so.1.0
33	lib/ugene/libU2Remote.so.1.0.0
34	lib/ugene/libU2Script.so	34	lib/ugene/libU2Script.so
35	lib/ugene/libU2Script.so.1	35	lib/ugene/libU2Script.so.1
36	lib/ugene/libU2Script.so.1.0	36	lib/ugene/libU2Script.so.1.0
Lines 43-52 Link Here
43	lib/ugene/libU2View.so.1	43	lib/ugene/libU2View.so.1
44	lib/ugene/libU2View.so.1.0	44	lib/ugene/libU2View.so.1.0
45	lib/ugene/libU2View.so.1.0.0	45	lib/ugene/libU2View.so.1.0.0
46	lib/ugene/libgtest.so
47	lib/ugene/libgtest.so.1
48	lib/ugene/libgtest.so.1.0
49	lib/ugene/libgtest.so.1.0.0
50	lib/ugene/libugenedb.so	46	lib/ugene/libugenedb.so
51	lib/ugene/libugenedb.so.1	47	lib/ugene/libugenedb.so.1
52	lib/ugene/libugenedb.so.1.0	48	lib/ugene/libugenedb.so.1.0
Lines 53-58 Link Here
53	lib/ugene/libugenedb.so.1.0.0	49	lib/ugene/libugenedb.so.1.0.0
54	lib/ugene/plugins/CoreTests.license	50	lib/ugene/plugins/CoreTests.license
55	lib/ugene/plugins/CoreTests.plugin	51	lib/ugene/plugins/CoreTests.plugin
		52	lib/ugene/plugins/GUITestBase.license
		53	lib/ugene/plugins/GUITestBase.plugin
56	lib/ugene/plugins/annotator.license	54	lib/ugene/plugins/annotator.license
57	lib/ugene/plugins/annotator.plugin	55	lib/ugene/plugins/annotator.plugin
58	lib/ugene/plugins/api_tests.license	56	lib/ugene/plugins/api_tests.license
Lines 67-74 Link Here
67	lib/ugene/plugins/chroma_view.plugin	65	lib/ugene/plugins/chroma_view.plugin
68	lib/ugene/plugins/circular_view.license	66	lib/ugene/plugins/circular_view.license
69	lib/ugene/plugins/circular_view.plugin	67	lib/ugene/plugins/circular_view.plugin
		68	lib/ugene/plugins/clark_support.license
		69	lib/ugene/plugins/clark_support.plugin
70	lib/ugene/plugins/dbi_bam.license	70	lib/ugene/plugins/dbi_bam.license
71	lib/ugene/plugins/dbi_bam.plugin	71	lib/ugene/plugins/dbi_bam.plugin
		72	lib/ugene/plugins/diamond_support.license
		73	lib/ugene/plugins/diamond_support.plugin
72	lib/ugene/plugins/dna_export.license	74	lib/ugene/plugins/dna_export.license
73	lib/ugene/plugins/dna_export.plugin	75	lib/ugene/plugins/dna_export.plugin
74	lib/ugene/plugins/dna_flexibility.license	76	lib/ugene/plugins/dna_flexibility.license
Lines 89-102 Link Here
89	lib/ugene/plugins/gor4.plugin	91	lib/ugene/plugins/gor4.plugin
90	lib/ugene/plugins/hmm2.license	92	lib/ugene/plugins/hmm2.license
91	lib/ugene/plugins/hmm2.plugin	93	lib/ugene/plugins/hmm2.plugin
92	%%SSE2%%lib/ugene/plugins/hmm3.license
93	%%SSE2%%lib/ugene/plugins/hmm3.plugin
94	lib/ugene/plugins/kalign.license	94	lib/ugene/plugins/kalign.license
95	lib/ugene/plugins/kalign.plugin	95	lib/ugene/plugins/kalign.plugin
		96	lib/ugene/plugins/kraken_support.license
		97	lib/ugene/plugins/kraken_support.plugin
96	lib/ugene/plugins/libCoreTests.so	98	lib/ugene/plugins/libCoreTests.so
97	lib/ugene/plugins/libCoreTests.so.1	99	lib/ugene/plugins/libCoreTests.so.1
98	lib/ugene/plugins/libCoreTests.so.1.0	100	lib/ugene/plugins/libCoreTests.so.1.0
99	lib/ugene/plugins/libCoreTests.so.1.0.0	101	lib/ugene/plugins/libCoreTests.so.1.0.0
		102	lib/ugene/plugins/libGUITestBase.so
		103	lib/ugene/plugins/libGUITestBase.so.1
		104	lib/ugene/plugins/libGUITestBase.so.1.0
		105	lib/ugene/plugins/libGUITestBase.so.1.0.0
100	lib/ugene/plugins/libannotator.so	106	lib/ugene/plugins/libannotator.so
101	lib/ugene/plugins/libannotator.so.1	107	lib/ugene/plugins/libannotator.so.1
102	lib/ugene/plugins/libannotator.so.1.0	108	lib/ugene/plugins/libannotator.so.1.0
Lines 125-134 Link Here
125	lib/ugene/plugins/libcircular_view.so.1	131	lib/ugene/plugins/libcircular_view.so.1
126	lib/ugene/plugins/libcircular_view.so.1.0	132	lib/ugene/plugins/libcircular_view.so.1.0
127	lib/ugene/plugins/libcircular_view.so.1.0.0	133	lib/ugene/plugins/libcircular_view.so.1.0.0
		134	lib/ugene/plugins/libclark_support.so
		135	lib/ugene/plugins/libclark_support.so.1
		136	lib/ugene/plugins/libclark_support.so.1.0
		137	lib/ugene/plugins/libclark_support.so.1.0.0
128	lib/ugene/plugins/libdbi_bam.so	138	lib/ugene/plugins/libdbi_bam.so
129	lib/ugene/plugins/libdbi_bam.so.1	139	lib/ugene/plugins/libdbi_bam.so.1
130	lib/ugene/plugins/libdbi_bam.so.1.0	140	lib/ugene/plugins/libdbi_bam.so.1.0
131	lib/ugene/plugins/libdbi_bam.so.1.0.0	141	lib/ugene/plugins/libdbi_bam.so.1.0.0
		142	lib/ugene/plugins/libdiamond_support.so
		143	lib/ugene/plugins/libdiamond_support.so.1
		144	lib/ugene/plugins/libdiamond_support.so.1.0
		145	lib/ugene/plugins/libdiamond_support.so.1.0.0
132	lib/ugene/plugins/libdna_export.so	146	lib/ugene/plugins/libdna_export.so
133	lib/ugene/plugins/libdna_export.so.1	147	lib/ugene/plugins/libdna_export.so.1
134	lib/ugene/plugins/libdna_export.so.1.0	148	lib/ugene/plugins/libdna_export.so.1.0
Lines 169-186 Link Here
169	lib/ugene/plugins/libhmm2.so.1	183	lib/ugene/plugins/libhmm2.so.1
170	lib/ugene/plugins/libhmm2.so.1.0	184	lib/ugene/plugins/libhmm2.so.1.0
171	lib/ugene/plugins/libhmm2.so.1.0.0	185	lib/ugene/plugins/libhmm2.so.1.0.0
172	%%SSE2%%lib/ugene/plugins/libhmm3.so
173	%%SSE2%%lib/ugene/plugins/libhmm3.so.1
174	%%SSE2%%lib/ugene/plugins/libhmm3.so.1.0
175	%%SSE2%%lib/ugene/plugins/libhmm3.so.1.0.0
176	lib/ugene/plugins/libkalign.so	186	lib/ugene/plugins/libkalign.so
177	lib/ugene/plugins/libkalign.so.1	187	lib/ugene/plugins/libkalign.so.1
178	lib/ugene/plugins/libkalign.so.1.0	188	lib/ugene/plugins/libkalign.so.1.0
179	lib/ugene/plugins/libkalign.so.1.0.0	189	lib/ugene/plugins/libkalign.so.1.0.0
		190	lib/ugene/plugins/libkraken_support.so
		191	lib/ugene/plugins/libkraken_support.so.1
		192	lib/ugene/plugins/libkraken_support.so.1.0
		193	lib/ugene/plugins/libkraken_support.so.1.0.0
180	lib/ugene/plugins/liblinkdata_support.so	194	lib/ugene/plugins/liblinkdata_support.so
181	lib/ugene/plugins/liblinkdata_support.so.1	195	lib/ugene/plugins/liblinkdata_support.so.1
182	lib/ugene/plugins/liblinkdata_support.so.1.0	196	lib/ugene/plugins/liblinkdata_support.so.1.0
183	lib/ugene/plugins/liblinkdata_support.so.1.0.0	197	lib/ugene/plugins/liblinkdata_support.so.1.0.0
		198	lib/ugene/plugins/libngs_reads_classification.so
		199	lib/ugene/plugins/libngs_reads_classification.so.1
		200	lib/ugene/plugins/libngs_reads_classification.so.1.0
		201	lib/ugene/plugins/libngs_reads_classification.so.1.0.0
184	lib/ugene/plugins/libopencl_support.so	202	lib/ugene/plugins/libopencl_support.so
185	lib/ugene/plugins/libopencl_support.so.1	203	lib/ugene/plugins/libopencl_support.so.1
186	lib/ugene/plugins/libopencl_support.so.1.0	204	lib/ugene/plugins/libopencl_support.so.1.0
Lines 221-230 Link Here
221	lib/ugene/plugins/libremote_blast.so.1	239	lib/ugene/plugins/libremote_blast.so.1
222	lib/ugene/plugins/libremote_blast.so.1.0	240	lib/ugene/plugins/libremote_blast.so.1.0
223	lib/ugene/plugins/libremote_blast.so.1.0.0	241	lib/ugene/plugins/libremote_blast.so.1.0.0
224	lib/ugene/plugins/libremote_service.so
225	lib/ugene/plugins/libremote_service.so.1
226	lib/ugene/plugins/libremote_service.so.1.0
227	lib/ugene/plugins/libremote_service.so.1.0.0
228	lib/ugene/plugins/librepeat_finder.so	242	lib/ugene/plugins/librepeat_finder.so
229	lib/ugene/plugins/librepeat_finder.so.1	243	lib/ugene/plugins/librepeat_finder.so.1
230	lib/ugene/plugins/librepeat_finder.so.1.0	244	lib/ugene/plugins/librepeat_finder.so.1.0
Lines 241-250 Link Here
241	lib/ugene/plugins/libtest_runner.so.1	255	lib/ugene/plugins/libtest_runner.so.1
242	lib/ugene/plugins/libtest_runner.so.1.0	256	lib/ugene/plugins/libtest_runner.so.1.0
243	lib/ugene/plugins/libtest_runner.so.1.0.0	257	lib/ugene/plugins/libtest_runner.so.1.0.0
244	%%NOX64%%lib/ugene/plugins/libumuscle.so	258	lib/ugene/plugins/libumuscle.so
245	%%NOX64%%lib/ugene/plugins/libumuscle.so.1	259	lib/ugene/plugins/libumuscle.so.1
246	%%NOX64%%lib/ugene/plugins/libumuscle.so.1.0	260	lib/ugene/plugins/libumuscle.so.1.0
247	%%NOX64%%lib/ugene/plugins/libumuscle.so.1.0.0	261	lib/ugene/plugins/libumuscle.so.1.0.0
248	lib/ugene/plugins/libvariants.so	262	lib/ugene/plugins/libvariants.so
249	lib/ugene/plugins/libvariants.so.1	263	lib/ugene/plugins/libvariants.so.1
250	lib/ugene/plugins/libvariants.so.1.0	264	lib/ugene/plugins/libvariants.so.1.0
Lines 253-258 Link Here
253	lib/ugene/plugins/libweight_matrix.so.1	267	lib/ugene/plugins/libweight_matrix.so.1
254	lib/ugene/plugins/libweight_matrix.so.1.0	268	lib/ugene/plugins/libweight_matrix.so.1.0
255	lib/ugene/plugins/libweight_matrix.so.1.0.0	269	lib/ugene/plugins/libweight_matrix.so.1.0.0
		270	lib/ugene/plugins/libwevote_support.so
		271	lib/ugene/plugins/libwevote_support.so.1
		272	lib/ugene/plugins/libwevote_support.so.1.0
		273	lib/ugene/plugins/libwevote_support.so.1.0.0
256	lib/ugene/plugins/libworkflow_designer.so	274	lib/ugene/plugins/libworkflow_designer.so
257	lib/ugene/plugins/libworkflow_designer.so.1	275	lib/ugene/plugins/libworkflow_designer.so.1
258	lib/ugene/plugins/libworkflow_designer.so.1.0	276	lib/ugene/plugins/libworkflow_designer.so.1.0
Lines 259-264 Link Here
259	lib/ugene/plugins/libworkflow_designer.so.1.0.0	277	lib/ugene/plugins/libworkflow_designer.so.1.0.0
260	lib/ugene/plugins/linkdata_support.license	278	lib/ugene/plugins/linkdata_support.license
261	lib/ugene/plugins/linkdata_support.plugin	279	lib/ugene/plugins/linkdata_support.plugin
		280	lib/ugene/plugins/ngs_reads_classification.license
		281	lib/ugene/plugins/ngs_reads_classification.plugin
262	lib/ugene/plugins/opencl_support.license	282	lib/ugene/plugins/opencl_support.license
263	lib/ugene/plugins/opencl_support.plugin	283	lib/ugene/plugins/opencl_support.plugin
264	lib/ugene/plugins/orf_marker.license	284	lib/ugene/plugins/orf_marker.license
Lines 279-286 Link Here
279	lib/ugene/plugins/query_designer.plugin	299	lib/ugene/plugins/query_designer.plugin
280	lib/ugene/plugins/remote_blast.license	300	lib/ugene/plugins/remote_blast.license
281	lib/ugene/plugins/remote_blast.plugin	301	lib/ugene/plugins/remote_blast.plugin
282	lib/ugene/plugins/remote_service.license
283	lib/ugene/plugins/remote_service.plugin
284	lib/ugene/plugins/repeat_finder.license	302	lib/ugene/plugins/repeat_finder.license
285	lib/ugene/plugins/repeat_finder.plugin	303	lib/ugene/plugins/repeat_finder.plugin
286	lib/ugene/plugins/sitecon.license	304	lib/ugene/plugins/sitecon.license
Lines 289-300 Link Here
289	lib/ugene/plugins/smith_waterman.plugin	307	lib/ugene/plugins/smith_waterman.plugin
290	lib/ugene/plugins/test_runner.license	308	lib/ugene/plugins/test_runner.license
291	lib/ugene/plugins/test_runner.plugin	309	lib/ugene/plugins/test_runner.plugin
292	%%NOX64%%lib/ugene/plugins/umuscle.license	310	lib/ugene/plugins/umuscle.license
293	%%NOX64%%lib/ugene/plugins/umuscle.plugin	311	lib/ugene/plugins/umuscle.plugin
294	lib/ugene/plugins/variants.license	312	lib/ugene/plugins/variants.license
295	lib/ugene/plugins/variants.plugin	313	lib/ugene/plugins/variants.plugin
296	lib/ugene/plugins/weight_matrix.license	314	lib/ugene/plugins/weight_matrix.license
297	lib/ugene/plugins/weight_matrix.plugin	315	lib/ugene/plugins/weight_matrix.plugin
		316	lib/ugene/plugins/wevote_support.license
		317	lib/ugene/plugins/wevote_support.plugin
298	lib/ugene/plugins/workflow_designer.license	318	lib/ugene/plugins/workflow_designer.license
299	lib/ugene/plugins/workflow_designer.plugin	319	lib/ugene/plugins/workflow_designer.plugin
300	lib/ugene/plugins_checker	320	lib/ugene/plugins_checker
Lines 306-317 Link Here
306	lib/ugene/ugeneui	326	lib/ugene/ugeneui
307	man/man1/ugene.1.gz	327	man/man1/ugene.1.gz
308	share/applications/ugene.desktop	328	share/applications/ugene.desktop
309	share/icons/application-x-ugene-ext.png	329	share/icons/hicolor/32x32/mimetypes/application-x-ugene-ext.png
310	share/mime/application-x-ugene.xml	330	share/mime/packages/application-x-ugene.xml
311	share/pixmaps/ugene.png	331	share/pixmaps/ugene.png
312	share/pixmaps/ugene.xpm	332	share/pixmaps/ugene.xpm
313	%%DATADIR%%/DBXRefRegistry.txt	333	%%DATADIR%%/DBXRefRegistry.txt
314	%%DATADIR%%/adapters/adapters.fasta	334	%%DATADIR%%/adapters/adapters.fasta
		335	%%DATADIR%%/adapters/illumina/NexteraPE-PE.fa
		336	%%DATADIR%%/adapters/illumina/TruSeq2-PE.fa
		337	%%DATADIR%%/adapters/illumina/TruSeq2-SE.fa
		338	%%DATADIR%%/adapters/illumina/TruSeq3-PE-2.fa
		339	%%DATADIR%%/adapters/illumina/TruSeq3-PE.fa
		340	%%DATADIR%%/adapters/illumina/TruSeq3-SE.fa
315	%%DATADIR%%/back_translation/Bacteria/Arthrobacter_aurescens_TC1.cut	341	%%DATADIR%%/back_translation/Bacteria/Arthrobacter_aurescens_TC1.cut
316	%%DATADIR%%/back_translation/Bacteria/Bacillus_subtilis.cut	342	%%DATADIR%%/back_translation/Bacteria/Bacillus_subtilis.cut
317	%%DATADIR%%/back_translation/Bacteria/Escherichia_coli.cut	343	%%DATADIR%%/back_translation/Bacteria/Escherichia_coli.cut
Lines 357-362 Link Here
357	%%DATADIR%%/cmdline/align-kalign.uwl	383	%%DATADIR%%/cmdline/align-kalign.uwl
358	%%DATADIR%%/cmdline/align-mafft.uwl	384	%%DATADIR%%/cmdline/align-mafft.uwl
359	%%DATADIR%%/cmdline/align-tcoffee.uwl	385	%%DATADIR%%/cmdline/align-tcoffee.uwl
		386	%%DATADIR%%/cmdline/align-to-reference.uwl
360	%%DATADIR%%/cmdline/align.uwl	387	%%DATADIR%%/cmdline/align.uwl
361	%%DATADIR%%/cmdline/convert-msa.uwl	388	%%DATADIR%%/cmdline/convert-msa.uwl
362	%%DATADIR%%/cmdline/convert-seq.uwl	389	%%DATADIR%%/cmdline/convert-seq.uwl
Lines 372-377 Link Here
372	%%DATADIR%%/cmdline/generate-dna.uwl	399	%%DATADIR%%/cmdline/generate-dna.uwl
373	%%DATADIR%%/cmdline/hmm2-build.uwl	400	%%DATADIR%%/cmdline/hmm2-build.uwl
374	%%DATADIR%%/cmdline/hmm2-search.uwl	401	%%DATADIR%%/cmdline/hmm2-search.uwl
		402	%%DATADIR%%/cmdline/hmm3-build-and-search.uwl
375	%%DATADIR%%/cmdline/join-quality.uwl	403	%%DATADIR%%/cmdline/join-quality.uwl
376	%%DATADIR%%/cmdline/local-blast+.uwl	404	%%DATADIR%%/cmdline/local-blast+.uwl
377	%%DATADIR%%/cmdline/local-blast.uwl	405	%%DATADIR%%/cmdline/local-blast.uwl
Lines 1150-1155 Link Here
1150	%%DATADIR%%/samples/ABIF/A01.abi	1178	%%DATADIR%%/samples/ABIF/A01.abi
1151	%%DATADIR%%/samples/ACE/BL060C3.ace	1179	%%DATADIR%%/samples/ACE/BL060C3.ace
1152	%%DATADIR%%/samples/ACE/K26.ace	1180	%%DATADIR%%/samples/ACE/K26.ace
		1181	%%DATADIR%%/samples/APR/DNA.apr
		1182	%%DATADIR%%/samples/APR/gyrA.apr
1153	%%DATADIR%%/samples/Assembly/chrM.fa	1183	%%DATADIR%%/samples/Assembly/chrM.fa
1154	%%DATADIR%%/samples/Assembly/chrM.sam	1184	%%DATADIR%%/samples/Assembly/chrM.sam
1155	%%DATADIR%%/samples/Assembly/chrM.sorted.bam	1185	%%DATADIR%%/samples/Assembly/chrM.sorted.bam
Lines 1393-1410 Link Here
1393	%%DATADIR%%/workflow_samples/Data merging/tfbs.uwl	1423	%%DATADIR%%/workflow_samples/Data merging/tfbs.uwl
1394	%%DATADIR%%/workflow_samples/HMMER/build-test-HMM.uwl	1424	%%DATADIR%%/workflow_samples/HMMER/build-test-HMM.uwl
1395	%%DATADIR%%/workflow_samples/HMMER/searchHMM.uwl	1425	%%DATADIR%%/workflow_samples/HMMER/searchHMM.uwl
1396	%%DATADIR%%/workflow_samples/NGS/assembly/spades_paired.uwl
1397	%%DATADIR%%/workflow_samples/NGS/assembly/spades_single.uwl
1398	%%DATADIR%%/workflow_samples/NGS/assembly.uwl
1399	%%DATADIR%%/workflow_samples/NGS/call_variants.uwl
1400	%%DATADIR%%/workflow_samples/NGS/chipseq_coverage.uwl	1426	%%DATADIR%%/workflow_samples/NGS/chipseq_coverage.uwl
		1427	%%DATADIR%%/workflow_samples/NGS/cistrome.uwl
1401	%%DATADIR%%/workflow_samples/NGS/cistrome/chip_seq.uwl	1428	%%DATADIR%%/workflow_samples/NGS/cistrome/chip_seq.uwl
1402	%%DATADIR%%/workflow_samples/NGS/cistrome/chip_seq_with_control.uwl	1429	%%DATADIR%%/workflow_samples/NGS/cistrome/chip_seq_with_control.uwl
1403	%%DATADIR%%/workflow_samples/NGS/cistrome.uwl
1404	%%DATADIR%%/workflow_samples/NGS/consensus.uwl	1430	%%DATADIR%%/workflow_samples/NGS/consensus.uwl
1405	%%DATADIR%%/workflow_samples/NGS/extract_coverage.uwl	1431	%%DATADIR%%/workflow_samples/NGS/extract_coverage.uwl
1406	%%DATADIR%%/workflow_samples/NGS/extract_transcript_seq.uwl	1432	%%DATADIR%%/workflow_samples/NGS/extract_transcript_seq.uwl
1407	%%DATADIR%%/workflow_samples/NGS/fastqc.uwl	1433	%%DATADIR%%/workflow_samples/NGS/fastqc.uwl
		1434	%%DATADIR%%/workflow_samples/NGS/from_tools_menu_only/ngs_assembly.uwl
		1435	%%DATADIR%%/workflow_samples/NGS/from_tools_menu_only/ngs_classification.uwl
		1436	%%DATADIR%%/workflow_samples/NGS/ngs_assembly_illumina_pe.uwl
		1437	%%DATADIR%%/workflow_samples/NGS/ngs_assembly_illumina_pe_nanopore.uwl
		1438	%%DATADIR%%/workflow_samples/NGS/ngs_assembly_illumina_se.uwl
		1439	%%DATADIR%%/workflow_samples/NGS/ngs_classification/ngs_classification_de_novo/ngs_classification_de_novo_paired.uwl
		1440	%%DATADIR%%/workflow_samples/NGS/ngs_classification/ngs_classification_de_novo/ngs_classification_de_novo_single.uwl
		1441	%%DATADIR%%/workflow_samples/NGS/ngs_classification/ngs_classification_parallel/ngs_classification_parallel_paired.uwl
		1442	%%DATADIR%%/workflow_samples/NGS/ngs_classification/ngs_classification_parallel/ngs_classification_parallel_single.uwl
		1443	%%DATADIR%%/workflow_samples/NGS/ngs_classification/ngs_classification_serial/ngs_classification_serial_paired.uwl
		1444	%%DATADIR%%/workflow_samples/NGS/ngs_classification/ngs_classification_serial/ngs_classification_serial_single.uwl
		1445	%%DATADIR%%/workflow_samples/NGS/ngs_classification_de_novo.uwl
		1446	%%DATADIR%%/workflow_samples/NGS/ngs_classification_parallel.uwl
		1447	%%DATADIR%%/workflow_samples/NGS/ngs_classification_serial.uwl
		1448	%%DATADIR%%/workflow_samples/NGS/ngs_transcriptomics_tophat_stringtie.uwl
		1449	%%DATADIR%%/workflow_samples/NGS/ngs_transcriptomics_tuxedo.uwl
		1450	%%DATADIR%%/workflow_samples/NGS/ngs_variant_annotation.uwl
		1451	%%DATADIR%%/workflow_samples/NGS/ngs_variant_calling.uwl
		1452	%%DATADIR%%/workflow_samples/NGS/ngs_variant_calling_full.uwl
1408	%%DATADIR%%/workflow_samples/NGS/raw_chip.uwl	1453	%%DATADIR%%/workflow_samples/NGS/raw_chip.uwl
1409	%%DATADIR%%/workflow_samples/NGS/raw_dna.uwl	1454	%%DATADIR%%/workflow_samples/NGS/raw_dna.uwl
1410	%%DATADIR%%/workflow_samples/NGS/raw_ngs/chipseq/chipseq_paired.uwl	1455	%%DATADIR%%/workflow_samples/NGS/raw_ngs/chipseq/chipseq_paired.uwl
Lines 1422-1430 Link Here
1422	%%DATADIR%%/workflow_samples/NGS/tuxedo/tuxedo_no_novel_transcr_paired.uwl	1467	%%DATADIR%%/workflow_samples/NGS/tuxedo/tuxedo_no_novel_transcr_paired.uwl
1423	%%DATADIR%%/workflow_samples/NGS/tuxedo/tuxedo_single_dataset.uwl	1468	%%DATADIR%%/workflow_samples/NGS/tuxedo/tuxedo_single_dataset.uwl
1424	%%DATADIR%%/workflow_samples/NGS/tuxedo/tuxedo_single_dataset_paired.uwl	1469	%%DATADIR%%/workflow_samples/NGS/tuxedo/tuxedo_single_dataset_paired.uwl
1425	%%DATADIR%%/workflow_samples/NGS/tuxedo.uwl
1426	%%DATADIR%%/workflow_samples/NGS/unmapped_reads.uwl	1470	%%DATADIR%%/workflow_samples/NGS/unmapped_reads.uwl
1427	%%DATADIR%%/workflow_samples/NGS/variation_annotation.uwl
1428	%%DATADIR%%/workflow_samples/Sanger sequencing/trim-and-align.uwl	1471	%%DATADIR%%/workflow_samples/Sanger sequencing/trim-and-align.uwl
1429	%%DATADIR%%/workflow_samples/Scenarios/filter_matched.uwl	1472	%%DATADIR%%/workflow_samples/Scenarios/filter_matched.uwl
1430	%%DATADIR%%/workflow_samples/Scenarios/find_inverted_repeats.uwl	1473	%%DATADIR%%/workflow_samples/Scenarios/find_inverted_repeats.uwl
Lines 1432-1437 Link Here
1432	%%DATADIR%%/workflow_samples/Scenarios/gene_by_gene_report.uwl	1475	%%DATADIR%%/workflow_samples/Scenarios/gene_by_gene_report.uwl
1433	%%DATADIR%%/workflow_samples/Scenarios/group_primers_pairs.uwl	1476	%%DATADIR%%/workflow_samples/Scenarios/group_primers_pairs.uwl
1434	%%DATADIR%%/workflow_samples/Scenarios/intersect_annotations.uwl	1477	%%DATADIR%%/workflow_samples/Scenarios/intersect_annotations.uwl
		1478	%%DATADIR%%/workflow_samples/Scenarios/length_filter.uwl
1435	%%DATADIR%%/workflow_samples/Scenarios/merge_sequence_annotation.uwl	1479	%%DATADIR%%/workflow_samples/Scenarios/merge_sequence_annotation.uwl
1436	%%DATADIR%%/workflow_samples/Scenarios/pcr.uwl	1480	%%DATADIR%%/workflow_samples/Scenarios/pcr.uwl
1437	%%DATADIR%%/workflow_samples/Scenarios/remote_blasting.uwl	1481	%%DATADIR%%/workflow_samples/Scenarios/remote_blasting.uwl
Lines 1442-1447 Link Here
1442	%%DATADIR%%/workflow_samples/users/FASTQ Trimmer.usa	1486	%%DATADIR%%/workflow_samples/users/FASTQ Trimmer.usa
1443	%%DATADIR%%/workflow_samples/users/Get the first half of sequence.usa	1487	%%DATADIR%%/workflow_samples/users/Get the first half of sequence.usa
1444	%%DATADIR%%/workflow_samples/users/Get the second half of sequence.usa	1488	%%DATADIR%%/workflow_samples/users/Get the second half of sequence.usa
		1489	%%DATADIR%%/workflow_samples/users/LengthMarker.usa
1445	%%DATADIR%%/workflow_samples/users/LinkData Fetch.usa	1490	%%DATADIR%%/workflow_samples/users/LinkData Fetch.usa
1446	%%DATADIR%%/workflow_samples/users/QualityFilter.usa	1491	%%DATADIR%%/workflow_samples/users/QualityFilter.usa
1447	%%DATADIR%%/workflow_samples/users/Read one sequence.usa	1492	%%DATADIR%%/workflow_samples/users/Read one sequence.usa

Return to bug 229463

Lines 2-9 Link Here

(-)biology/ugene/Makefile (-19 / +12 lines)
2	# $FreeBSD$	2	# $FreeBSD$
3		3
4	PORTNAME= ugene	4	PORTNAME= ugene
5	DISTVERSION= 1.22.0	5	DISTVERSION= 1.31.0
6	PORTREVISION= 3
7	CATEGORIES= biology science	6	CATEGORIES= biology science
8	MASTER_SITES= http://ugene.unipro.ru/downloads/	7	MASTER_SITES= http://ugene.unipro.ru/downloads/
9	DISTFILES= ${DISTNAME}${EXTRACT_SUFX} QueryDesigner_UserManual.pdf \	8	DISTFILES= ${DISTNAME}${EXTRACT_SUFX} QueryDesigner_UserManual.pdf \
Lines 14-30 Link Here
14	MAINTAINER= h2+fbsdports@fsfe.org	13	MAINTAINER= h2+fbsdports@fsfe.org
15	COMMENT= Free, open-source, cross-platform bioinformatics toolkit	14	COMMENT= Free, open-source, cross-platform bioinformatics toolkit
16		15
17	LICENSE= GPLv2	16	LICENSE= GPLv2+
		17	LICENSE_FILE= ${WRKSRC}/LICENSE.txt
18		18
19	RUN_DEPENDS= bash:shells/bash	19	RUN_DEPENDS= bash:shells/bash
20		20
21	BROKEN_aarch64= Fails to build: invokes x86 asm	21	BROKEN_aarch64= Fails to build: invokes x86 asm
22		22
23	USES= desktop-file-utils qmake qt:5	23	USES= desktop-file-utils qmake qt:5 shared-mime-info
24	USE_GL= glu	24	USE_GL= gl glu
25	USE_QT= buildtools_build linguisttools_build scripttools_build \	25	USE_QT= buildtools_build linguisttools_build \
26	gui network printsupport script sql svg webkit widgets xml \	26	core gui network opengl printsupport script scripttools \
		27	sql svg testlib webkit widgets xml \
27	imageformats_run	28	imageformats_run
		29	USE_XORG= x11 xtst
28		30
29	QMAKE_ARGS= INSTALL_PREFIX="${PREFIX}" UGENE_INSTALL_DATA="${DATADIR}" \	31	QMAKE_ARGS= INSTALL_PREFIX="${PREFIX}" UGENE_INSTALL_DATA="${DATADIR}" \
30	INSTALL_MANDIR="${MAN1PREFIX}/man" LRELEASE="${LRELEASE}" \	32	INSTALL_MANDIR="${MAN1PREFIX}/man" LRELEASE="${LRELEASE}" \
Lines 31-59 Link Here
31	LUPDATE="${LUPDATE}"	33	LUPDATE="${LUPDATE}"
32	ALL_TARGET= release	34	ALL_TARGET= release
33		35
34	# Required for Google Test code
35	CXXFLAGS+= -std=c++11
36
37	DOCSDIR= ${DATADIR}/manuals	36	DOCSDIR= ${DATADIR}/manuals
38		37
39	OPTIONS_DEFINE= DOCS	38	OPTIONS_DEFINE= DOCS OPENCL
40	DOCS_DESC= Install official UGENE documentation (PDF)	39	DOCS_DESC= Install official UGENE documentation (PDF)
41		40
		41	OPENCL_QMAKE_ON= UGENE_OPENCL_DETECTED=1
		42
42	.include <bsd.port.pre.mk>	43	.include <bsd.port.pre.mk>
43		44
44	.if ${ARCH} == amd64	45	.if ${ARCH} == amd64
45	# XXX: need to manually tell the build we are on x64	46	# XXX: need to manually tell the build we are on x64
46	QMAKE_ARGS+= CONFIG+=x64	47	QMAKE_ARGS+= CONFIG+=x64
47	PLIST_SUB+= NOX64="@comment "
48	.else
49	PLIST_SUB+= NOX64=""
50	.endif	48	.endif
51		49
52	.if ${MACHINE_CPU:Msse2}	50	.if ${MACHINE_CPU:Msse2}
53	QMAKE_ARGS+= UGENE_SSE2_DETECTED=1	51	QMAKE_ARGS+= UGENE_SSE2_DETECTED=1
54	PLIST_SUB+= SSE2=""
55	.else
56	PLIST_SUB+= SSE2="@comment "
57	.endif	52	.endif
58		53
59	post-extract:	54	post-extract:
Lines 67-74 Link Here
67	${WRKSRC}/installer/_common_data/ugene	62	${WRKSRC}/installer/_common_data/ugene
68	@${REINPLACE_CMD} -e 's\|-bit version\|& for ${OPSYS}/${ARCH}\|' \	63	@${REINPLACE_CMD} -e 's\|-bit version\|& for ${OPSYS}/${ARCH}\|' \
69	${WRKSRC}/src/ugeneui/src/main_window/AboutDialogController.cpp	64	${WRKSRC}/src/ugeneui/src/main_window/AboutDialogController.cpp
70	@${REINPLACE_CMD} -e '/unix_not_mac/,+11d' \
71	${WRKSRC}/src/corelibs/U2Core/U2Core.pri
72	@${REINPLACE_CMD} 's, -lbreakpad,,' \	65	@${REINPLACE_CMD} 's, -lbreakpad,,' \
73	${WRKSRC}/src/corelibs/U2Private/U2Private.pri \	66	${WRKSRC}/src/corelibs/U2Private/U2Private.pri \
74	${WRKSRC}/src/plugins_checker/plugins_checker.pri \	67	${WRKSRC}/src/plugins_checker/plugins_checker.pri \

Lines 1-30 Link Here

(-)biology/ugene/files/patch-git_279756e4 (-30 lines)
1	From 279756e448f53af5a495a2ce3a12abdf833fc703 Mon Sep 17 00:00:00 2001
2	From: Kevin Kofler <kevin.kofler@chello.at>
3	Date: Tue, 2 Jan 2018 22:21:03 +0100
4	Subject: [PATCH] Fix build against Qt 5.10
5	MIME-Version: 1.0
6	Content-Type: text/plain; charset=UTF-8
7	Content-Transfer-Encoding: 8bit
8
9	src/plugins/external_tool_support/src/bowtie2/Bowtie2Settings.ui: Remove
10	shortcut setting that breaks the build with Qt 5.10.
11
12	UGENE can be built with Qt ≥ 5.6 and a separate QtWebKit. With Qt 5.10,
13	we were hitting a build error: uic was producing code that did not
14	compile.
15	---
16	src/plugins/external_tool_support/src/bowtie2/Bowtie2Settings.ui \| 3 ---
17	1 file changed, 3 deletions(-)
18
19	--- src/plugins/external_tool_support/src/ui/Bowtie2Settings.ui
20	+++ src/plugins/external_tool_support/src/ui/Bowtie2Settings.ui
21	@@ -254,9 +254,6 @@
22	<property name="text">
23	<string>Disallow gaps (--gbar)</string>
24	</property>
25	- <property name="shortcut">
26	- <string notr="true"/>
27	- </property>
28	</widget>
29	</item>
30	</layout>

Line 0 Link Here

(-)biology/ugene/files/patch-git_578c949 (+25 lines)
	1	From 578c949ae7df017e23c3eda0293faa3db718c89f Mon Sep 17 00:00:00 2001
	2	From: Yuliya Algaer <yalgaer@gmail.com>
	3	Date: Fri, 24 Aug 2018 21:24:12 +0700
	4	Subject: [PATCH] Build fix for Fedora
	5
	6	--- src/plugins/external_tool_support/src/trimmomatic/util/LengthSettingsWidget.cpp.orig 2018-08-16 13:58:58 UTC
	7	+++ src/plugins/external_tool_support/src/trimmomatic/util/LengthSettingsWidget.cpp
	8	@@ -20,6 +20,7 @@
	9	*/
	10
	11	#include <U2Core/U2SafePoints.h>
	12	+#include <QIntValidator>
	13
	14	#include "LengthSettingsWidget.h"
	15	#include "LineEditHighlighter.h"
	16	--- src/plugins/external_tool_support/src/trimmomatic/util/QualitySettingsWidget.cpp.orig 2018-08-16 13:58:58 UTC
	17	+++ src/plugins/external_tool_support/src/trimmomatic/util/QualitySettingsWidget.cpp
	18	@@ -19,6 +19,7 @@
	19	* MA 02110-1301, USA.
	20	*/
	21
	22	+#include <QIntValidator>
	23	#include <U2Core/U2SafePoints.h>
	24
	25	#include "QualitySettingsWidget.h"

Lines 1-4 Link Here

(-)biology/ugene/files/patch-src_corelibs_U2Private_U2Private.pro (-16 / +10 lines)
1	--- src/corelibs/U2Private/U2Private.pro.orig 2016-03-31 12:22:14 UTC	1	--- src/corelibs/U2Private/U2Private.pro.orig 2018-08-16 13:59:12 UTC
2	+++ src/corelibs/U2Private/U2Private.pro	2	+++ src/corelibs/U2Private/U2Private.pro
3	@@ -12,12 +12,7 @@ HEADERS += src/AppContextImpl.h \	3	@@ -12,12 +12,7 @@ HEADERS += src/AppContextImpl.h \
4	src/PluginSupportImpl.h \	4	src/PluginSupportImpl.h \
Lines 14-20 Link Here
14		14
15	SOURCES += src/AppContextImpl.cpp \	15	SOURCES += src/AppContextImpl.cpp \
16	src/AppSettingsImpl.cpp \	16	src/AppSettingsImpl.cpp \
17	@@ -30,29 +25,7 @@ SOURCES += src/AppContextImpl.cpp \	17	@@ -30,23 +25,13 @@ SOURCES += src/AppContextImpl.cpp \
18	src/PluginSupportImpl.cpp \	18	src/PluginSupportImpl.cpp \
19	src/ServiceRegistryImpl.cpp \	19	src/ServiceRegistryImpl.cpp \
20	src/SettingsImpl.cpp \	20	src/SettingsImpl.cpp \
Lines 26-47 Link Here
26	- src/crash_handler/StackWalker.cpp	26	- src/crash_handler/StackWalker.cpp
27	+ src/TaskSchedulerImpl.cpp	27	+ src/TaskSchedulerImpl.cpp
28		28
29	TRANSLATIONS += transl/english.ts \	29	TRANSLATIONS += transl/russian.ts
30	transl/russian.ts	30
31	-	31	win32 {
32	-win32 {	32	HEADERS += src/crash_handler/CrashHandlerPrivateWin.h
33	- HEADERS += src/crash_handler/CrashHandlerPrivateWin.h	33	SOURCES += src/crash_handler/CrashHandlerPrivateWin.cpp
34	- SOURCES += src/crash_handler/CrashHandlerPrivateWin.cpp
35	-}	34	-}
36	-	35	-
37	-unix_not_mac() {	36	-unix_not_mac() {
38	- HEADERS += src/crash_handler/CrashHandlerPrivateUnixNotMac.h	37	- HEADERS += src/crash_handler/CrashHandlerPrivateUnixNotMac.h
39	- SOURCES += src/crash_handler/CrashHandlerPrivateUnixNotMac.cpp	38	- SOURCES += src/crash_handler/CrashHandlerPrivateUnixNotMac.cpp
40	-}	39	}
41	-	40
42	-mac {	41	mac {
43	- HEADERS += src/crash_handler/CrashHandlerPrivateMac.h \
44	- src/SleepPreventerMac.h
45	- SOURCES += src/crash_handler/CrashHandlerPrivateMac.cpp \
46	- src/SleepPreventerMac.cpp
47	-}

Line 0 Link Here

(-)biology/ugene/files/patch-src_libs__3rdparty_QSpec_src_drivers_GTKeyboardDriverLinux.cpp (+22 lines)
	1	Use the Linux driver for FreeBSD as well. Fixes crash on startup.
	2
	3	--- src/libs_3rdparty/QSpec/src/drivers/GTKeyboardDriverLinux.cpp.orig 2018-09-02 00:22:54 UTC
	4	+++ src/libs_3rdparty/QSpec/src/drivers/GTKeyboardDriverLinux.cpp
	5	@@ -22,7 +22,7 @@
	6	#include <cctype>
	7	#include "GTKeyboardDriver.h"
	8
	9	-#if defined __linux__
	10	+#if defined(__linux__) \|\| defined(__FreeBSD__)
	11	#define XK_LATIN1 // for latin symbol
	12	#define XK_MISCELLANY // for action keys
	13	#include <X11/keysymdef.h>
	14	@@ -31,7 +31,7 @@
	15
	16	namespace HI {
	17
	18	-#if defined __linux__
	19	+#if defined(__linux__) \|\| defined(__FreeBSD__)
	20
	21	#define GT_CLASS_NAME "GTKeyboardDriverLinux"
	22

Lines 1-14 Link Here

(-)biology/ugene/files/patch-src_plugins__3rdparty_umuscle_src_MuscleWorkPool.cpp (-14 lines)
1	--- src/plugins_3rdparty/umuscle/src/MuscleWorkPool.cpp.orig 2016-03-31 12:22:09 UTC
2	+++ src/plugins_3rdparty/umuscle/src/MuscleWorkPool.cpp
3	@@ -28,9 +28,10 @@ namespace U2 {
4
5	MuscleWorkPool::MuscleWorkPool(MuscleContext *_ctx, const MuscleTaskSettings &_config, TaskStateInfo& _ti, int _nThreads, const MAlignment& _ma, MAlignment& _res, bool _mhack)
6	:ctx(_ctx), config(_config), ma(_ma), res(_res), mhack(_mhack), Weights(NULL), ProgNodes(NULL), ph(NULL), ti(_ti),
7	- treeNodeStatus(NULL), treeNodeIndexes(NULL), nThreads(_nThreads), uJoin(0), ptrbOscillating(false), bAnyAccepted(false), InternalNodeIndexes(NULL), uInternalNodeCount(0),
8	+ treeNodeStatus(NULL), treeNodeIndexes(NULL), nThreads(_nThreads), uJoin(0), bAnyAccepted(false), InternalNodeIndexes(NULL), uInternalNodeCount(0),
9	bReversed(false), bRight(false), History(NULL), bLockLeft(NULL), bLockRight(false), msaIn(NULL)
10	{
11	+ *ptrbOscillating = false;
12	refineConstructot();
13	}
14	MuscleWorkPool::~MuscleWorkPool() {

Lines 1-13 Link Here

(-)biology/ugene/files/patch-src_ugene__globals.pri (-13 lines)
1	--- src/ugene_globals.pri.orig 2016-03-31 12:22:21 UTC
2	+++ src/ugene_globals.pri
3	@@ -8,8 +8,8 @@ DEFINES+=UGENE_VER_MAJOR=$${UGENE_VER_MA
4	DEFINES+=UGENE_VER_MINOR=$${UGENE_VER_MINOR}
5	DEFINES+=UGENE_VER_PATCH=$${UGENE_VER_PATCH}
6
7	-unix : !macx : INCLUDEPATH-=/usr/include
8	-unix : !macx : INCLUDEPATH+=/usr/include/qt5 /usr/include
9	+#unix : !macx : INCLUDEPATH-=/usr/include
10	+#unix : !macx : INCLUDEPATH+=/usr/include/qt5 /usr/include
11	#unix : !macx : INCLUDEPATH =/usr/include/qt5 $$INCLUDEPATH
12
13	# NGS package

Lines 1-4 Link Here

(-)biology/ugene/files/patch-ugene.pro (-10 / +11 lines)
1	--- ugene.pro.orig 2016-03-31 12:21:56 UTC	1	--- ugene.pro.orig 2018-08-16 13:58:51 UTC
2	+++ ugene.pro	2	+++ ugene.pro
3	@@ -20,7 +20,6 @@ use_bundled_zlib() {	3	@@ -20,7 +20,6 @@ use_bundled_zlib() {
4	}	4	}
Lines 7-25 Link Here
7	- src/libs_3rdparty/breakpad \	7	- src/libs_3rdparty/breakpad \
8	src/libs_3rdparty/qscore \	8	src/libs_3rdparty/qscore \
9	src/libs_3rdparty/sqlite3 \	9	src/libs_3rdparty/sqlite3 \
10	src/libs_3rdparty/gtest \	10	src/libs_3rdparty/samtools \
11	@@ -144,15 +143,8 @@ UGENE_TRANSL_QM_TARGET_DIR = $$OUT_PWD/s	11	@@ -141,16 +140,8 @@ UGENE_TRANSL_QM_TARGET_DIR = $$OUT_PWD/src/_debug $$OU
12	win32 : UGENE_DEV_NULL = nul	12	win32 : UGENE_DEV_NULL = nul
13	unix : UGENE_DEV_NULL = /dev/null	13	unix : UGENE_DEV_NULL = /dev/null
14		14
15	-UGENE_LRELEASE =	15	-UGENE_LRELEASE =
16	-UGENE_LUPDATE =	16	-UGENE_LUPDATE =
17	-system(lrelease-qt5 -version > $$UGENE_DEV_NULL 2> $$UGENE_DEV_NULL) {	17	-message(Using QT from $$[QT_INSTALL_BINS])
18	- UGENE_LRELEASE = lrelease-qt5	18	-system($$[QT_INSTALL_BINS]/lrelease-qt5 -version > $$UGENE_DEV_NULL 2> $$UGENE_DEV_NULL) {
19	- UGENE_LUPDATE = lupdate-qt5	19	- UGENE_LRELEASE = $$[QT_INSTALL_BINS]/lrelease-qt5
20	-} else : system(lrelease -version > $$UGENE_DEV_NULL 2> $$UGENE_DEV_NULL) {	20	- UGENE_LUPDATE = $$[QT_INSTALL_BINS]/lupdate-qt5
21	- UGENE_LRELEASE = lrelease	21	-} else : system($$[QT_INSTALL_BINS]/lrelease -version > $$UGENE_DEV_NULL 2> $$UGENE_DEV_NULL) {
22	- UGENE_LUPDATE = lupdate	22	- UGENE_LRELEASE = $$[QT_INSTALL_BINS]/lrelease
		23	- UGENE_LUPDATE = $$[QT_INSTALL_BINS]/lupdate
23	-}	24	-}
24	+UGENE_LRELEASE = $$LRELEASE	25	+UGENE_LRELEASE = $$LRELEASE
25	+UGENE_LUPDATE = $$LUPDATE	26	+UGENE_LUPDATE = $$LUPDATE