Attachment 196793 Details for Bug 229463 – Update biology/ugene to 1.31.0

[patch] Update biology/ugene to 1.31.0

ugene-1.31.0.diff (text/plain), 35.41 KB, created by Jason E. Hale on 2018-09-02 15:15:59 UTC

(hide)

Description:

Filename:

MIME Type:

Creator: Jason E. Hale

Created: 2018-09-02 15:15:59 UTC

Size: 35.41 KB

patch

obsolete

>Index: biology/ugene/Makefile
>===================================================================
>--- biology/ugene/Makefile	(revision 478615)
>+++ biology/ugene/Makefile	(working copy)
>@@ -2,8 +2,7 @@
> # $FreeBSD$
> 
> PORTNAME=	ugene
>-DISTVERSION=	1.22.0
>-PORTREVISION=	3
>+DISTVERSION=	1.31.0
> CATEGORIES=	biology science
> MASTER_SITES=	http://ugene.unipro.ru/downloads/
> DISTFILES=	${DISTNAME}${EXTRACT_SUFX} QueryDesigner_UserManual.pdf \
>@@ -14,17 +13,20 @@
> MAINTAINER=	h2+fbsdports@fsfe.org
> COMMENT=	Free, open-source, cross-platform bioinformatics toolkit
> 
>-LICENSE=	GPLv2
>+LICENSE=	GPLv2+
>+LICENSE_FILE=	${WRKSRC}/LICENSE.txt
> 
> RUN_DEPENDS=	bash:shells/bash
> 
> BROKEN_aarch64=	Fails to build: invokes x86 asm
> 
>-USES=		desktop-file-utils qmake qt:5
>-USE_GL=		glu
>-USE_QT=		buildtools_build linguisttools_build scripttools_build \
>-		gui network printsupport script sql svg webkit widgets xml \
>+USES=		desktop-file-utils qmake qt:5 shared-mime-info
>+USE_GL=		gl glu
>+USE_QT=		buildtools_build linguisttools_build \
>+		core gui network opengl printsupport script scripttools \
>+		sql svg testlib webkit widgets xml \
> 		imageformats_run
>+USE_XORG=	x11 xtst
> 
> QMAKE_ARGS=	INSTALL_PREFIX="${PREFIX}" UGENE_INSTALL_DATA="${DATADIR}" \
> 		INSTALL_MANDIR="${MAN1PREFIX}/man" LRELEASE="${LRELEASE}" \
>@@ -31,29 +33,22 @@
> 		LUPDATE="${LUPDATE}"
> ALL_TARGET=	release
> 
>-# Required for Google Test code
>-CXXFLAGS+=	-std=c++11
>-
> DOCSDIR=	${DATADIR}/manuals
> 
>-OPTIONS_DEFINE=	DOCS
>+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:
>@@ -67,8 +62,6 @@
> 		${WRKSRC}/installer/_common_data/ugene
> 	@${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 \
>Index: biology/ugene/distinfo
>===================================================================
>--- biology/ugene/distinfo	(revision 478615)
>+++ biology/ugene/distinfo	(working copy)
>@@ -1,5 +1,6 @@
>-SHA256 (ugene/ugene-1.22.0.tar.gz) = ee46be799c9f02a9b6a89f13747a4918d5c96c01676dc2d4cc4a4c98278912b6
>-SIZE (ugene/ugene-1.22.0.tar.gz) = 20986853
>+TIMESTAMP = 1535840965
>+SHA256 (ugene/ugene-1.31.0.tar.gz) = d1f46306834a292618cc54b31060b69da5b0b18da311a55bf82ab42f5a434320
>+SIZE (ugene/ugene-1.31.0.tar.gz) = 20656562
> SHA256 (ugene/QueryDesigner_UserManual.pdf) = 5d232c0de7e9d1fd32b8ee0a78f9f4abe1ab9d6536ec3958c47de29f3096faf4
> SIZE (ugene/QueryDesigner_UserManual.pdf) = 855662
> SHA256 (ugene/UniproUGENE_UserManual.pdf) = ae6aef32a6e92a30ba7c36cdd894a8caf634d678f15da7ad9eab52b6f40b9ed6
>Index: biology/ugene/files/patch-git_279756e4
>===================================================================
>--- biology/ugene/files/patch-git_279756e4	(revision 478615)
>+++ biology/ugene/files/patch-git_279756e4	(nonexistent)
>@@ -1,30 +0,0 @@
>-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 â¥ 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>
>
>Property changes on: biology/ugene/files/patch-git_279756e4
>___________________________________________________________________
>Deleted: fbsd:nokeywords
>## -1 +0,0 ##
>-yes
>\ No newline at end of property
>Deleted: svn:eol-style
>## -1 +0,0 ##
>-native
>\ No newline at end of property
>Deleted: svn:mime-type
>## -1 +0,0 ##
>-text/plain
>\ No newline at end of property
>Index: biology/ugene/files/patch-git_578c949
>===================================================================
>--- biology/ugene/files/patch-git_578c949	(nonexistent)
>+++ biology/ugene/files/patch-git_578c949	(working copy)
>@@ -0,0 +1,25 @@
>+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"
>
>Property changes on: biology/ugene/files/patch-git_578c949
>___________________________________________________________________
>Added: fbsd:nokeywords
>## -0,0 +1 ##
>+yes
>\ No newline at end of property
>Added: svn:eol-style
>## -0,0 +1 ##
>+native
>\ No newline at end of property
>Added: svn:mime-type
>## -0,0 +1 ##
>+text/plain
>\ No newline at end of property
>Index: biology/ugene/files/patch-src_corelibs_U2Private_U2Private.pro
>===================================================================
>--- biology/ugene/files/patch-src_corelibs_U2Private_U2Private.pro	(revision 478615)
>+++ biology/ugene/files/patch-src_corelibs_U2Private_U2Private.pro	(working copy)
>@@ -1,4 +1,4 @@
>---- src/corelibs/U2Private/U2Private.pro.orig	2016-03-31 12:22:14 UTC
>+--- 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 \
>@@ -14,7 +14,7 @@
>  
>  SOURCES += src/AppContextImpl.cpp \
>             src/AppSettingsImpl.cpp \
>-@@ -30,29 +25,7 @@ SOURCES += src/AppContextImpl.cpp \
>+@@ -30,23 +25,13 @@ SOURCES += src/AppContextImpl.cpp \
>             src/PluginSupportImpl.cpp \
>             src/ServiceRegistryImpl.cpp \
>             src/SettingsImpl.cpp \
>@@ -26,22 +26,16 @@
> -           src/crash_handler/StackWalker.cpp
> +           src/TaskSchedulerImpl.cpp
>  
>- TRANSLATIONS += transl/english.ts \
>-                 transl/russian.ts
>--
>--win32 {
>--    HEADERS += src/crash_handler/CrashHandlerPrivateWin.h
>--    SOURCES += src/crash_handler/CrashHandlerPrivateWin.cpp
>+ TRANSLATIONS += transl/russian.ts
>+ 
>+ win32 {
>+     HEADERS += src/crash_handler/CrashHandlerPrivateWin.h
>+     SOURCES += src/crash_handler/CrashHandlerPrivateWin.cpp
> -}
> -
> -unix_not_mac() {
> -    HEADERS += src/crash_handler/CrashHandlerPrivateUnixNotMac.h
> -    SOURCES += src/crash_handler/CrashHandlerPrivateUnixNotMac.cpp
>--}
>--
>--mac {
>--    HEADERS += src/crash_handler/CrashHandlerPrivateMac.h \
>--               src/SleepPreventerMac.h
>--    SOURCES += src/crash_handler/CrashHandlerPrivateMac.cpp \
>--               src/SleepPreventerMac.cpp
>--}
>+ }
>+ 
>+ mac {
>Index: biology/ugene/files/patch-src_libs__3rdparty_QSpec_src_drivers_GTKeyboardDriverLinux.cpp
>===================================================================
>--- biology/ugene/files/patch-src_libs__3rdparty_QSpec_src_drivers_GTKeyboardDriverLinux.cpp	(nonexistent)
>+++ biology/ugene/files/patch-src_libs__3rdparty_QSpec_src_drivers_GTKeyboardDriverLinux.cpp	(working copy)
>@@ -0,0 +1,22 @@
>+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"
>+ 
>
>Property changes on: biology/ugene/files/patch-src_libs__3rdparty_QSpec_src_drivers_GTKeyboardDriverLinux.cpp
>___________________________________________________________________
>Added: fbsd:nokeywords
>## -0,0 +1 ##
>+yes
>\ No newline at end of property
>Added: svn:eol-style
>## -0,0 +1 ##
>+native
>\ No newline at end of property
>Added: svn:mime-type
>## -0,0 +1 ##
>+text/plain
>\ No newline at end of property
>Index: biology/ugene/files/patch-src_libs__3rdparty_QSpec_src_drivers_GTMouseDriverLinux.cpp
>===================================================================
>--- biology/ugene/files/patch-src_libs__3rdparty_QSpec_src_drivers_GTMouseDriverLinux.cpp	(nonexistent)
>+++ biology/ugene/files/patch-src_libs__3rdparty_QSpec_src_drivers_GTMouseDriverLinux.cpp	(working copy)
>@@ -0,0 +1,20 @@
>+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);
>
>Property changes on: biology/ugene/files/patch-src_libs__3rdparty_QSpec_src_drivers_GTMouseDriverLinux.cpp
>___________________________________________________________________
>Added: fbsd:nokeywords
>## -0,0 +1 ##
>+yes
>\ No newline at end of property
>Added: svn:eol-style
>## -0,0 +1 ##
>+native
>\ No newline at end of property
>Added: svn:mime-type
>## -0,0 +1 ##
>+text/plain
>\ No newline at end of property
>Index: biology/ugene/files/patch-src_libs__3rdparty_samtools_samtools.pri
>===================================================================
>--- biology/ugene/files/patch-src_libs__3rdparty_samtools_samtools.pri	(revision 478615)
>+++ biology/ugene/files/patch-src_libs__3rdparty_samtools_samtools.pri	(nonexistent)
>@@ -1,11 +0,0 @@
>---- src/libs_3rdparty/samtools/samtools.pri.orig	2016-03-31 12:21:56 UTC
>-+++ src/libs_3rdparty/samtools/samtools.pri
>-@@ -3,7 +3,7 @@ UGENE_RELATIVE_DESTDIR = ''
>- 
>- TEMPLATE = lib
>- CONFIG +=thread debug_and_release staticlib warn_off
>--INCLUDEPATH += src src/samtools ../../include /usr/include
>-+INCLUDEPATH += src src/samtools ../../include
>- win32 : INCLUDEPATH += src/samtools/win32
>- DEFINES+="_FILE_OFFSET_BITS=64" _LARGEFILE64_SOURCE _USE_KNETFILE
>- win32 : DEFINES += _USE_MATH_DEFINES "inline=__inline" "__func__=__FUNCTION__" "R_OK=4" "atoll=_atoi64" "alloca=_alloca"
>
>Property changes on: biology/ugene/files/patch-src_libs__3rdparty_samtools_samtools.pri
>___________________________________________________________________
>Deleted: fbsd:nokeywords
>## -1 +0,0 ##
>-yes
>\ No newline at end of property
>Deleted: svn:eol-style
>## -1 +0,0 ##
>-native
>\ No newline at end of property
>Deleted: svn:mime-type
>## -1 +0,0 ##
>-text/plain
>\ No newline at end of property
>Index: biology/ugene/files/patch-src_plugins__3rdparty_phylip_src_phylip.h
>===================================================================
>--- biology/ugene/files/patch-src_plugins__3rdparty_phylip_src_phylip.h	(revision 478615)
>+++ biology/ugene/files/patch-src_plugins__3rdparty_phylip_src_phylip.h	(nonexistent)
>@@ -1,10 +0,0 @@
>---- src/plugins_3rdparty/phylip/src/phylip.h.orig	2017-12-30 19:54:56 UTC
>-+++ src/plugins_3rdparty/phylip/src/phylip.h
>-@@ -271,7 +271,6 @@ MALLOCRETURN    *mymalloc(long);
>- #define MAXNCH          30   /* must be greater than or equal to nmlngth */
>- #define maxcategs       9    /* maximum number of site types */
>- #define maxcategs2     11    /* maximum number of site types + 2 */
>--#define point           "."
>- #define pointe          '.'
>- #define down            2
>- #define MAXSHIMOTREES 100
>
>Property changes on: biology/ugene/files/patch-src_plugins__3rdparty_phylip_src_phylip.h
>___________________________________________________________________
>Deleted: fbsd:nokeywords
>## -1 +0,0 ##
>-yes
>\ No newline at end of property
>Deleted: svn:eol-style
>## -1 +0,0 ##
>-native
>\ No newline at end of property
>Deleted: svn:mime-type
>## -1 +0,0 ##
>-text/plain
>\ No newline at end of property
>Index: biology/ugene/files/patch-src_plugins__3rdparty_umuscle_src_MuscleWorkPool.cpp
>===================================================================
>--- biology/ugene/files/patch-src_plugins__3rdparty_umuscle_src_MuscleWorkPool.cpp	(revision 478615)
>+++ biology/ugene/files/patch-src_plugins__3rdparty_umuscle_src_MuscleWorkPool.cpp	(nonexistent)
>@@ -1,14 +0,0 @@
>---- 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() {
>
>Property changes on: biology/ugene/files/patch-src_plugins__3rdparty_umuscle_src_MuscleWorkPool.cpp
>___________________________________________________________________
>Deleted: fbsd:nokeywords
>## -1 +0,0 ##
>-yes
>\ No newline at end of property
>Deleted: svn:eol-style
>## -1 +0,0 ##
>-native
>\ No newline at end of property
>Deleted: svn:mime-type
>## -1 +0,0 ##
>-text/plain
>\ No newline at end of property
>Index: biology/ugene/files/patch-src_plugins__3rdparty_variants_variants.pri
>===================================================================
>--- biology/ugene/files/patch-src_plugins__3rdparty_variants_variants.pri	(revision 478615)
>+++ biology/ugene/files/patch-src_plugins__3rdparty_variants_variants.pri	(nonexistent)
>@@ -1,11 +0,0 @@
>---- src/plugins_3rdparty/variants/variants.pri.orig	2016-03-31 12:22:09 UTC
>-+++ src/plugins_3rdparty/variants/variants.pri
>-@@ -20,7 +20,7 @@ use_bundled_zlib() {
>- win32 : LIBS += -lwsock32
>- 
>- 
>--INCLUDEPATH += src ../../include /usr/include
>-+INCLUDEPATH += src ../../include
>- INCLUDEPATH += ../../libs_3rdparty/samtools/src/samtools 
>- INCLUDEPATH += ../../libs_3rdparty/samtools/src
>- INCLUDEPATH += ../../libs_3rdparty/samtools/src/samtools/bcftools
>
>Property changes on: biology/ugene/files/patch-src_plugins__3rdparty_variants_variants.pri
>___________________________________________________________________
>Deleted: fbsd:nokeywords
>## -1 +0,0 ##
>-yes
>\ No newline at end of property
>Deleted: svn:eol-style
>## -1 +0,0 ##
>-native
>\ No newline at end of property
>Deleted: svn:mime-type
>## -1 +0,0 ##
>-text/plain
>\ No newline at end of property
>Index: biology/ugene/files/patch-src_plugins__checker_src_Main.cpp
>===================================================================
>--- biology/ugene/files/patch-src_plugins__checker_src_Main.cpp	(revision 478615)
>+++ biology/ugene/files/patch-src_plugins__checker_src_Main.cpp	(working copy)
>@@ -1,4 +1,4 @@
>---- src/plugins_checker/src/Main.cpp.orig	2016-03-31 12:22:09 UTC
>+--- src/plugins_checker/src/Main.cpp.orig	2018-08-16 13:59:06 UTC
> +++ src/plugins_checker/src/Main.cpp
> @@ -39,7 +39,7 @@
>  #include <ServiceRegistryImpl.h>
>@@ -20,7 +20,7 @@
>  
>      const char* build = QT_VERSION_STR, *runtime = qVersion();
>      if (strcmp(build, runtime) > 0){
>-@@ -140,7 +142,7 @@ int main(int argc, char **argv)
>+@@ -141,7 +143,7 @@ int main(int argc, char **argv)
>      delete cmdLineRegistry;
>      appContext->setCMDLineRegistry(NULL);
>  
>Index: biology/ugene/files/patch-src_ugene__globals.pri
>===================================================================
>--- biology/ugene/files/patch-src_ugene__globals.pri	(revision 478615)
>+++ biology/ugene/files/patch-src_ugene__globals.pri	(nonexistent)
>@@ -1,13 +0,0 @@
>---- 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
>
>Property changes on: biology/ugene/files/patch-src_ugene__globals.pri
>___________________________________________________________________
>Deleted: fbsd:nokeywords
>## -1 +0,0 ##
>-yes
>\ No newline at end of property
>Deleted: svn:eol-style
>## -1 +0,0 ##
>-native
>\ No newline at end of property
>Deleted: svn:mime-type
>## -1 +0,0 ##
>-text/plain
>\ No newline at end of property
>Index: biology/ugene/files/patch-src_ugenecl_src_Main.cpp
>===================================================================
>--- biology/ugene/files/patch-src_ugenecl_src_Main.cpp	(revision 478615)
>+++ biology/ugene/files/patch-src_ugenecl_src_Main.cpp	(working copy)
>@@ -1,6 +1,6 @@
>---- src/ugenecl/src/Main.cpp.orig	2016-03-31 12:22:19 UTC
>+--- src/ugenecl/src/Main.cpp.orig	2018-08-16 13:59:20 UTC
> +++ src/ugenecl/src/Main.cpp
>-@@ -94,7 +94,7 @@
>+@@ -93,7 +93,7 @@
>  #include <ServiceRegistryImpl.h>
>  #include <SettingsImpl.h>
>  #include <TaskSchedulerImpl.h>
>@@ -9,7 +9,7 @@
>  
>  // local project imports
>  #include "DumpHelpTask.h"
>-@@ -192,9 +192,11 @@ static void setSearchPaths() {
>+@@ -191,6 +191,7 @@ static void setSearchPaths() {
>  
>  int main(int argc, char **argv)
>  {
>@@ -17,10 +17,14 @@
>      if (CrashHandler::isEnabled()) {
>          CrashHandler::setupHandler();
>      }
>+@@ -198,6 +199,7 @@ int main(int argc, char **argv)
>+     if (qgetenv(ENV_SEND_CRASH_REPORTS) == "0") {
>+         CrashHandler::setSendCrashReports(false);
>+     }
> +#endif
>+ 
>      const char* build = QT_VERSION_STR, *runtime = qVersion();
>      if (strcmp(build, runtime) > 0){
>-         printf("Installed Qt version must be %s or greater \r\n", QT_VERSION_STR);
> @@ -617,7 +619,7 @@ int main(int argc, char **argv)
>      delete pwr;
>      appContext->setAlignmentAlgorithmsRegistry(NULL);
>Index: biology/ugene/files/patch-src_ugeneui_src_Main.cpp
>===================================================================
>--- biology/ugene/files/patch-src_ugeneui_src_Main.cpp	(revision 478615)
>+++ biology/ugene/files/patch-src_ugeneui_src_Main.cpp	(working copy)
>@@ -1,6 +1,6 @@
>---- src/ugeneui/src/Main.cpp.orig	2016-03-31 12:22:18 UTC
>+--- src/ugeneui/src/Main.cpp.orig	2018-08-16 13:59:19 UTC
> +++ src/ugeneui/src/Main.cpp
>-@@ -134,7 +134,7 @@
>+@@ -136,7 +136,7 @@
>  #include <ServiceRegistryImpl.h>
>  #include <SettingsImpl.h>
>  #include <TaskSchedulerImpl.h>
>@@ -9,7 +9,7 @@
>  
>  #include "app_settings/AppSettingsGUIImpl.h"
>  #include "app_settings/logview_settings/LogSettingsGUIController.h"
>-@@ -343,9 +343,11 @@ void fixMacFonts() {
>+@@ -353,6 +353,7 @@ void fixMacFonts() {
>  
>  int main(int argc, char **argv)
>  {
>@@ -17,11 +17,15 @@
>      if (CrashHandler::isEnabled()) {
>          CrashHandler::setupHandler();
>      }
>+@@ -360,6 +361,7 @@ int main(int argc, char **argv)
>+     if (qgetenv(ENV_SEND_CRASH_REPORTS) == "0") {
>+         CrashHandler::setSendCrashReports(false);
>+     }
> +#endif
>  
>      QT_REQUIRE_VERSION( argc, argv, QT_VERSION_STR );
>  
>-@@ -966,7 +968,7 @@ int main(int argc, char **argv)
>+@@ -973,7 +975,7 @@ int main(int argc, char **argv)
>      }
>  
>      UgeneUpdater::onClose();
>Index: biology/ugene/files/patch-ugene.pro
>===================================================================
>--- biology/ugene/files/patch-ugene.pro	(revision 478615)
>+++ biology/ugene/files/patch-ugene.pro	(working copy)
>@@ -1,4 +1,4 @@
>---- ugene.pro.orig	2016-03-31 12:21:56 UTC
>+--- ugene.pro.orig	2018-08-16 13:58:51 UTC
> +++ ugene.pro
> @@ -20,7 +20,6 @@ use_bundled_zlib() {
>  }
>@@ -7,19 +7,20 @@
> -          src/libs_3rdparty/breakpad \
>            src/libs_3rdparty/qscore \
>            src/libs_3rdparty/sqlite3 \
>-           src/libs_3rdparty/gtest \
>-@@ -144,15 +143,8 @@ UGENE_TRANSL_QM_TARGET_DIR = $$OUT_PWD/s
>+           src/libs_3rdparty/samtools \
>+@@ -141,16 +140,8 @@ UGENE_TRANSL_QM_TARGET_DIR = $$OUT_PWD/src/_debug $$OU
>  win32 : UGENE_DEV_NULL = nul
>  unix : UGENE_DEV_NULL = /dev/null
>  
> -UGENE_LRELEASE =
>--UGENE_LUPDATE = 
>--system(lrelease-qt5 -version > $$UGENE_DEV_NULL 2> $$UGENE_DEV_NULL) {
>--    UGENE_LRELEASE = lrelease-qt5
>--    UGENE_LUPDATE = lupdate-qt5
>--} else : system(lrelease -version > $$UGENE_DEV_NULL 2> $$UGENE_DEV_NULL) {
>--    UGENE_LRELEASE = lrelease
>--    UGENE_LUPDATE = lupdate
>+-UGENE_LUPDATE =
>+-message(Using QT from $$[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
>Index: biology/ugene/pkg-plist
>===================================================================
>--- biology/ugene/pkg-plist	(revision 478615)
>+++ biology/ugene/pkg-plist	(working copy)
>@@ -1,4 +1,8 @@
> bin/ugene
>+lib/ugene/libQSpec.so
>+lib/ugene/libQSpec.so.1
>+lib/ugene/libQSpec.so.1.0
>+lib/ugene/libQSpec.so.1.0.0
> lib/ugene/libU2Algorithm.so
> lib/ugene/libU2Algorithm.so.1
> lib/ugene/libU2Algorithm.so.1.0
>@@ -27,10 +31,6 @@
> lib/ugene/libU2Private.so.1
> lib/ugene/libU2Private.so.1.0
> lib/ugene/libU2Private.so.1.0.0
>-lib/ugene/libU2Remote.so
>-lib/ugene/libU2Remote.so.1
>-lib/ugene/libU2Remote.so.1.0
>-lib/ugene/libU2Remote.so.1.0.0
> lib/ugene/libU2Script.so
> lib/ugene/libU2Script.so.1
> lib/ugene/libU2Script.so.1.0
>@@ -43,10 +43,6 @@
> lib/ugene/libU2View.so.1
> lib/ugene/libU2View.so.1.0
> lib/ugene/libU2View.so.1.0.0
>-lib/ugene/libgtest.so
>-lib/ugene/libgtest.so.1
>-lib/ugene/libgtest.so.1.0
>-lib/ugene/libgtest.so.1.0.0
> lib/ugene/libugenedb.so
> lib/ugene/libugenedb.so.1
> lib/ugene/libugenedb.so.1.0
>@@ -53,6 +49,8 @@
> lib/ugene/libugenedb.so.1.0.0
> lib/ugene/plugins/CoreTests.license
> lib/ugene/plugins/CoreTests.plugin
>+lib/ugene/plugins/GUITestBase.license
>+lib/ugene/plugins/GUITestBase.plugin
> lib/ugene/plugins/annotator.license
> lib/ugene/plugins/annotator.plugin
> lib/ugene/plugins/api_tests.license
>@@ -67,8 +65,12 @@
> lib/ugene/plugins/chroma_view.plugin
> lib/ugene/plugins/circular_view.license
> lib/ugene/plugins/circular_view.plugin
>+lib/ugene/plugins/clark_support.license
>+lib/ugene/plugins/clark_support.plugin
> lib/ugene/plugins/dbi_bam.license
> lib/ugene/plugins/dbi_bam.plugin
>+lib/ugene/plugins/diamond_support.license
>+lib/ugene/plugins/diamond_support.plugin
> lib/ugene/plugins/dna_export.license
> lib/ugene/plugins/dna_export.plugin
> lib/ugene/plugins/dna_flexibility.license
>@@ -89,14 +91,18 @@
> 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/kraken_support.license
>+lib/ugene/plugins/kraken_support.plugin
> lib/ugene/plugins/libCoreTests.so
> lib/ugene/plugins/libCoreTests.so.1
> lib/ugene/plugins/libCoreTests.so.1.0
> lib/ugene/plugins/libCoreTests.so.1.0.0
>+lib/ugene/plugins/libGUITestBase.so
>+lib/ugene/plugins/libGUITestBase.so.1
>+lib/ugene/plugins/libGUITestBase.so.1.0
>+lib/ugene/plugins/libGUITestBase.so.1.0.0
> lib/ugene/plugins/libannotator.so
> lib/ugene/plugins/libannotator.so.1
> lib/ugene/plugins/libannotator.so.1.0
>@@ -125,10 +131,18 @@
> lib/ugene/plugins/libcircular_view.so.1
> lib/ugene/plugins/libcircular_view.so.1.0
> lib/ugene/plugins/libcircular_view.so.1.0.0
>+lib/ugene/plugins/libclark_support.so
>+lib/ugene/plugins/libclark_support.so.1
>+lib/ugene/plugins/libclark_support.so.1.0
>+lib/ugene/plugins/libclark_support.so.1.0.0
> lib/ugene/plugins/libdbi_bam.so
> lib/ugene/plugins/libdbi_bam.so.1
> lib/ugene/plugins/libdbi_bam.so.1.0
> lib/ugene/plugins/libdbi_bam.so.1.0.0
>+lib/ugene/plugins/libdiamond_support.so
>+lib/ugene/plugins/libdiamond_support.so.1
>+lib/ugene/plugins/libdiamond_support.so.1.0
>+lib/ugene/plugins/libdiamond_support.so.1.0.0
> lib/ugene/plugins/libdna_export.so
> lib/ugene/plugins/libdna_export.so.1
> lib/ugene/plugins/libdna_export.so.1.0
>@@ -169,18 +183,22 @@
> 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/libkraken_support.so
>+lib/ugene/plugins/libkraken_support.so.1
>+lib/ugene/plugins/libkraken_support.so.1.0
>+lib/ugene/plugins/libkraken_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/libngs_reads_classification.so
>+lib/ugene/plugins/libngs_reads_classification.so.1
>+lib/ugene/plugins/libngs_reads_classification.so.1.0
>+lib/ugene/plugins/libngs_reads_classification.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
>@@ -221,10 +239,6 @@
> lib/ugene/plugins/libremote_blast.so.1
> lib/ugene/plugins/libremote_blast.so.1.0
> lib/ugene/plugins/libremote_blast.so.1.0.0
>-lib/ugene/plugins/libremote_service.so
>-lib/ugene/plugins/libremote_service.so.1
>-lib/ugene/plugins/libremote_service.so.1.0
>-lib/ugene/plugins/libremote_service.so.1.0.0
> lib/ugene/plugins/librepeat_finder.so
> lib/ugene/plugins/librepeat_finder.so.1
> lib/ugene/plugins/librepeat_finder.so.1.0
>@@ -241,10 +255,10 @@
> lib/ugene/plugins/libtest_runner.so.1
> lib/ugene/plugins/libtest_runner.so.1.0
> lib/ugene/plugins/libtest_runner.so.1.0.0
>-%%NOX64%%lib/ugene/plugins/libumuscle.so
>-%%NOX64%%lib/ugene/plugins/libumuscle.so.1
>-%%NOX64%%lib/ugene/plugins/libumuscle.so.1.0
>-%%NOX64%%lib/ugene/plugins/libumuscle.so.1.0.0
>+lib/ugene/plugins/libumuscle.so
>+lib/ugene/plugins/libumuscle.so.1
>+lib/ugene/plugins/libumuscle.so.1.0
>+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
>@@ -253,6 +267,10 @@
> lib/ugene/plugins/libweight_matrix.so.1
> lib/ugene/plugins/libweight_matrix.so.1.0
> lib/ugene/plugins/libweight_matrix.so.1.0.0
>+lib/ugene/plugins/libwevote_support.so
>+lib/ugene/plugins/libwevote_support.so.1
>+lib/ugene/plugins/libwevote_support.so.1.0
>+lib/ugene/plugins/libwevote_support.so.1.0.0
> lib/ugene/plugins/libworkflow_designer.so
> lib/ugene/plugins/libworkflow_designer.so.1
> lib/ugene/plugins/libworkflow_designer.so.1.0
>@@ -259,6 +277,8 @@
> lib/ugene/plugins/libworkflow_designer.so.1.0.0
> lib/ugene/plugins/linkdata_support.license
> lib/ugene/plugins/linkdata_support.plugin
>+lib/ugene/plugins/ngs_reads_classification.license
>+lib/ugene/plugins/ngs_reads_classification.plugin
> lib/ugene/plugins/opencl_support.license
> lib/ugene/plugins/opencl_support.plugin
> lib/ugene/plugins/orf_marker.license
>@@ -279,8 +299,6 @@
> lib/ugene/plugins/query_designer.plugin
> lib/ugene/plugins/remote_blast.license
> lib/ugene/plugins/remote_blast.plugin
>-lib/ugene/plugins/remote_service.license
>-lib/ugene/plugins/remote_service.plugin
> lib/ugene/plugins/repeat_finder.license
> lib/ugene/plugins/repeat_finder.plugin
> lib/ugene/plugins/sitecon.license
>@@ -289,12 +307,14 @@
> lib/ugene/plugins/smith_waterman.plugin
> 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/umuscle.license
>+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/wevote_support.license
>+lib/ugene/plugins/wevote_support.plugin
> lib/ugene/plugins/workflow_designer.license
> lib/ugene/plugins/workflow_designer.plugin
> lib/ugene/plugins_checker
>@@ -306,12 +326,18 @@
> lib/ugene/ugeneui
> man/man1/ugene.1.gz
> share/applications/ugene.desktop
>-share/icons/application-x-ugene-ext.png
>-share/mime/application-x-ugene.xml
>+share/icons/hicolor/32x32/mimetypes/application-x-ugene-ext.png
>+share/mime/packages/application-x-ugene.xml
> share/pixmaps/ugene.png
> share/pixmaps/ugene.xpm
> %%DATADIR%%/DBXRefRegistry.txt
> %%DATADIR%%/adapters/adapters.fasta
>+%%DATADIR%%/adapters/illumina/NexteraPE-PE.fa
>+%%DATADIR%%/adapters/illumina/TruSeq2-PE.fa
>+%%DATADIR%%/adapters/illumina/TruSeq2-SE.fa
>+%%DATADIR%%/adapters/illumina/TruSeq3-PE-2.fa
>+%%DATADIR%%/adapters/illumina/TruSeq3-PE.fa
>+%%DATADIR%%/adapters/illumina/TruSeq3-SE.fa
> %%DATADIR%%/back_translation/Bacteria/Arthrobacter_aurescens_TC1.cut
> %%DATADIR%%/back_translation/Bacteria/Bacillus_subtilis.cut
> %%DATADIR%%/back_translation/Bacteria/Escherichia_coli.cut
>@@ -357,6 +383,7 @@
> %%DATADIR%%/cmdline/align-kalign.uwl
> %%DATADIR%%/cmdline/align-mafft.uwl
> %%DATADIR%%/cmdline/align-tcoffee.uwl
>+%%DATADIR%%/cmdline/align-to-reference.uwl
> %%DATADIR%%/cmdline/align.uwl
> %%DATADIR%%/cmdline/convert-msa.uwl
> %%DATADIR%%/cmdline/convert-seq.uwl
>@@ -372,6 +399,7 @@
> %%DATADIR%%/cmdline/generate-dna.uwl
> %%DATADIR%%/cmdline/hmm2-build.uwl
> %%DATADIR%%/cmdline/hmm2-search.uwl
>+%%DATADIR%%/cmdline/hmm3-build-and-search.uwl
> %%DATADIR%%/cmdline/join-quality.uwl
> %%DATADIR%%/cmdline/local-blast+.uwl
> %%DATADIR%%/cmdline/local-blast.uwl
>@@ -1150,6 +1178,8 @@
> %%DATADIR%%/samples/ABIF/A01.abi
> %%DATADIR%%/samples/ACE/BL060C3.ace
> %%DATADIR%%/samples/ACE/K26.ace
>+%%DATADIR%%/samples/APR/DNA.apr
>+%%DATADIR%%/samples/APR/gyrA.apr
> %%DATADIR%%/samples/Assembly/chrM.fa
> %%DATADIR%%/samples/Assembly/chrM.sam
> %%DATADIR%%/samples/Assembly/chrM.sorted.bam
>@@ -1393,18 +1423,33 @@
> %%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/assembly/spades_paired.uwl
>-%%DATADIR%%/workflow_samples/NGS/assembly/spades_single.uwl
>-%%DATADIR%%/workflow_samples/NGS/assembly.uwl
>-%%DATADIR%%/workflow_samples/NGS/call_variants.uwl
> %%DATADIR%%/workflow_samples/NGS/chipseq_coverage.uwl
>+%%DATADIR%%/workflow_samples/NGS/cistrome.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/consensus.uwl
> %%DATADIR%%/workflow_samples/NGS/extract_coverage.uwl
> %%DATADIR%%/workflow_samples/NGS/extract_transcript_seq.uwl
> %%DATADIR%%/workflow_samples/NGS/fastqc.uwl
>+%%DATADIR%%/workflow_samples/NGS/from_tools_menu_only/ngs_assembly.uwl
>+%%DATADIR%%/workflow_samples/NGS/from_tools_menu_only/ngs_classification.uwl
>+%%DATADIR%%/workflow_samples/NGS/ngs_assembly_illumina_pe.uwl
>+%%DATADIR%%/workflow_samples/NGS/ngs_assembly_illumina_pe_nanopore.uwl
>+%%DATADIR%%/workflow_samples/NGS/ngs_assembly_illumina_se.uwl
>+%%DATADIR%%/workflow_samples/NGS/ngs_classification/ngs_classification_de_novo/ngs_classification_de_novo_paired.uwl
>+%%DATADIR%%/workflow_samples/NGS/ngs_classification/ngs_classification_de_novo/ngs_classification_de_novo_single.uwl
>+%%DATADIR%%/workflow_samples/NGS/ngs_classification/ngs_classification_parallel/ngs_classification_parallel_paired.uwl
>+%%DATADIR%%/workflow_samples/NGS/ngs_classification/ngs_classification_parallel/ngs_classification_parallel_single.uwl
>+%%DATADIR%%/workflow_samples/NGS/ngs_classification/ngs_classification_serial/ngs_classification_serial_paired.uwl
>+%%DATADIR%%/workflow_samples/NGS/ngs_classification/ngs_classification_serial/ngs_classification_serial_single.uwl
>+%%DATADIR%%/workflow_samples/NGS/ngs_classification_de_novo.uwl
>+%%DATADIR%%/workflow_samples/NGS/ngs_classification_parallel.uwl
>+%%DATADIR%%/workflow_samples/NGS/ngs_classification_serial.uwl
>+%%DATADIR%%/workflow_samples/NGS/ngs_transcriptomics_tophat_stringtie.uwl
>+%%DATADIR%%/workflow_samples/NGS/ngs_transcriptomics_tuxedo.uwl
>+%%DATADIR%%/workflow_samples/NGS/ngs_variant_annotation.uwl
>+%%DATADIR%%/workflow_samples/NGS/ngs_variant_calling.uwl
>+%%DATADIR%%/workflow_samples/NGS/ngs_variant_calling_full.uwl
> %%DATADIR%%/workflow_samples/NGS/raw_chip.uwl
> %%DATADIR%%/workflow_samples/NGS/raw_dna.uwl
> %%DATADIR%%/workflow_samples/NGS/raw_ngs/chipseq/chipseq_paired.uwl
>@@ -1422,9 +1467,7 @@
> %%DATADIR%%/workflow_samples/NGS/tuxedo/tuxedo_no_novel_transcr_paired.uwl
> %%DATADIR%%/workflow_samples/NGS/tuxedo/tuxedo_single_dataset.uwl
> %%DATADIR%%/workflow_samples/NGS/tuxedo/tuxedo_single_dataset_paired.uwl
>-%%DATADIR%%/workflow_samples/NGS/tuxedo.uwl
> %%DATADIR%%/workflow_samples/NGS/unmapped_reads.uwl
>-%%DATADIR%%/workflow_samples/NGS/variation_annotation.uwl
> %%DATADIR%%/workflow_samples/Sanger sequencing/trim-and-align.uwl
> %%DATADIR%%/workflow_samples/Scenarios/filter_matched.uwl
> %%DATADIR%%/workflow_samples/Scenarios/find_inverted_repeats.uwl
>@@ -1432,6 +1475,7 @@
> %%DATADIR%%/workflow_samples/Scenarios/gene_by_gene_report.uwl
> %%DATADIR%%/workflow_samples/Scenarios/group_primers_pairs.uwl
> %%DATADIR%%/workflow_samples/Scenarios/intersect_annotations.uwl
>+%%DATADIR%%/workflow_samples/Scenarios/length_filter.uwl
> %%DATADIR%%/workflow_samples/Scenarios/merge_sequence_annotation.uwl
> %%DATADIR%%/workflow_samples/Scenarios/pcr.uwl
> %%DATADIR%%/workflow_samples/Scenarios/remote_blasting.uwl
>@@ -1442,6 +1486,7 @@
> %%DATADIR%%/workflow_samples/users/FASTQ Trimmer.usa
> %%DATADIR%%/workflow_samples/users/Get the first half of sequence.usa
> %%DATADIR%%/workflow_samples/users/Get the second half of sequence.usa
>+%%DATADIR%%/workflow_samples/users/LengthMarker.usa
> %%DATADIR%%/workflow_samples/users/LinkData Fetch.usa
> %%DATADIR%%/workflow_samples/users/QualityFilter.usa
> %%DATADIR%%/workflow_samples/users/Read one sequence.usa

Flags:

jhale: maintainer-approval? (h2+fbsdports)

Actions: View | Diff

Attachments on bug 229463: 196793