Index: head/biology/ugene/Makefile =================================================================== --- head/biology/ugene/Makefile (revision 478817) +++ head/biology/ugene/Makefile (revision 478818) @@ -1,78 +1,71 @@ # Created by: Hannes Hauswedell # $FreeBSD$ 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 \ UniproUGENE_UserManual.pdf WorkflowDesigner_UserManual.pdf DIST_SUBDIR= ${PORTNAME} EXTRACT_ONLY= ${DISTNAME}${EXTRACT_SUFX} 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="${LRELEASE}" \ LUPDATE="${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 .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 ${MACHINE_CPU:Msse2} QMAKE_ARGS+= UGENE_SSE2_DETECTED=1 -PLIST_SUB+= SSE2="" -.else -PLIST_SUB+= SSE2="@comment " .endif post-extract: @${MKDIR} ${WRKSRC}/data/manuals ${CP} -p ${_DISTDIR}/*.pdf ${WRKSRC}/data/manuals post-patch: # yes, bash is required, stuff will not execute with sh @${REINPLACE_CMD} -e 's|/bin/bash|/usr/bin/env bash|' \ ${WRKSRC}/src/gen_bin_script.cmd \ ${WRKSRC}/installer/_common_data/ugene @${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 \ ${WRKSRC}/src/ugenecl/ugenecl.pri \ ${WRKSRC}/src/ugeneui/ugeneui.pri .include Index: head/biology/ugene/distinfo =================================================================== --- head/biology/ugene/distinfo (revision 478817) +++ head/biology/ugene/distinfo (revision 478818) @@ -1,8 +1,9 @@ -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 SIZE (ugene/UniproUGENE_UserManual.pdf) = 13443754 SHA256 (ugene/WorkflowDesigner_UserManual.pdf) = 8cc6630f62c82de42926c14c3d01ebc3c7d85ab7d9ec2a81e55a19740806735c SIZE (ugene/WorkflowDesigner_UserManual.pdf) = 29474484 Index: head/biology/ugene/files/patch-src_plugins__3rdparty_phylip_src_phylip.h =================================================================== --- head/biology/ugene/files/patch-src_plugins__3rdparty_phylip_src_phylip.h (revision 478817) +++ head/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: head/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: head/biology/ugene/files/patch-src_ugene__globals.pri =================================================================== --- head/biology/ugene/files/patch-src_ugene__globals.pri (revision 478817) +++ head/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: head/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: head/biology/ugene/files/patch-src_plugins__3rdparty_variants_variants.pri =================================================================== --- head/biology/ugene/files/patch-src_plugins__3rdparty_variants_variants.pri (revision 478817) +++ head/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: head/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: head/biology/ugene/files/patch-src_libs__3rdparty_samtools_samtools.pri =================================================================== --- head/biology/ugene/files/patch-src_libs__3rdparty_samtools_samtools.pri (revision 478817) +++ head/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: head/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: head/biology/ugene/files/patch-git_279756e4 =================================================================== --- head/biology/ugene/files/patch-git_279756e4 (revision 478817) +++ head/biology/ugene/files/patch-git_279756e4 (nonexistent) @@ -1,30 +0,0 @@ -From 279756e448f53af5a495a2ce3a12abdf833fc703 Mon Sep 17 00:00:00 2001 -From: Kevin Kofler -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 @@ - - Disallow gaps (--gbar) - -- -- -- - - - Property changes on: head/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: head/biology/ugene/files/patch-src_plugins__3rdparty_umuscle_src_MuscleWorkPool.cpp =================================================================== --- head/biology/ugene/files/patch-src_plugins__3rdparty_umuscle_src_MuscleWorkPool.cpp (revision 478817) +++ head/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: head/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: head/biology/ugene/files/patch-git_578c949 =================================================================== --- head/biology/ugene/files/patch-git_578c949 (nonexistent) +++ head/biology/ugene/files/patch-git_578c949 (revision 478818) @@ -0,0 +1,25 @@ +From 578c949ae7df017e23c3eda0293faa3db718c89f Mon Sep 17 00:00:00 2001 +From: Yuliya Algaer +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 ++#include + + #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 + #include + + #include "QualitySettingsWidget.h" Property changes on: head/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: head/biology/ugene/files/patch-src_corelibs_U2Private_U2Private.pro =================================================================== --- head/biology/ugene/files/patch-src_corelibs_U2Private_U2Private.pro (revision 478817) +++ head/biology/ugene/files/patch-src_corelibs_U2Private_U2Private.pro (revision 478818) @@ -1,47 +1,41 @@ ---- 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 \ src/ServiceRegistryImpl.h \ src/SettingsImpl.h \ - src/TaskSchedulerImpl.h \ - src/crash_handler/CrashHandler.h \ - src/crash_handler/CrashHandlerArgsHelper.h \ - src/crash_handler/CrashHandlerPrivate.h \ - src/crash_handler/CrashLogCache.h \ - src/crash_handler/StackWalker.h + src/TaskSchedulerImpl.h 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 \ - src/TaskSchedulerImpl.cpp \ - src/crash_handler/CrashHandler.cpp \ - src/crash_handler/CrashHandlerArgsHelper.cpp \ - src/crash_handler/CrashHandlerPrivate.cpp \ - src/crash_handler/CrashLogCache.cpp \ - 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: head/biology/ugene/files/patch-src_libs__3rdparty_QSpec_src_drivers_GTKeyboardDriverLinux.cpp =================================================================== --- head/biology/ugene/files/patch-src_libs__3rdparty_QSpec_src_drivers_GTKeyboardDriverLinux.cpp (nonexistent) +++ head/biology/ugene/files/patch-src_libs__3rdparty_QSpec_src_drivers_GTKeyboardDriverLinux.cpp (revision 478818) @@ -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 + #include "GTKeyboardDriver.h" + +-#if defined __linux__ ++#if defined(__linux__) || defined(__FreeBSD__) + #define XK_LATIN1 // for latin symbol + #define XK_MISCELLANY // for action keys + #include +@@ -31,7 +31,7 @@ + + namespace HI { + +-#if defined __linux__ ++#if defined(__linux__) || defined(__FreeBSD__) + + #define GT_CLASS_NAME "GTKeyboardDriverLinux" + Property changes on: head/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: head/biology/ugene/files/patch-src_libs__3rdparty_QSpec_src_drivers_GTMouseDriverLinux.cpp =================================================================== --- head/biology/ugene/files/patch-src_libs__3rdparty_QSpec_src_drivers_GTMouseDriverLinux.cpp (nonexistent) +++ head/biology/ugene/files/patch-src_libs__3rdparty_QSpec_src_drivers_GTMouseDriverLinux.cpp (revision 478818) @@ -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 + +-#ifdef __linux__ ++#if defined(__linux__) || defined(__FreeBSD__) + #include + #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: head/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: head/biology/ugene/files/patch-src_plugins__checker_src_Main.cpp =================================================================== --- head/biology/ugene/files/patch-src_plugins__checker_src_Main.cpp (revision 478817) +++ head/biology/ugene/files/patch-src_plugins__checker_src_Main.cpp (revision 478818) @@ -1,31 +1,31 @@ ---- 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 #include #include -#include +//#include #define TR_SETTINGS_ROOT QString("test_runner/") @@ -55,8 +55,10 @@ static void registerCoreServices() { int main(int argc, char **argv) { +#if 0 CrashHandler::setupHandler(); CrashHandler::setSendCrashReports(false); +#endif 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); - CrashHandler::shutdown(); + //CrashHandler::shutdown(); return rc; } Index: head/biology/ugene/files/patch-src_ugenecl_src_Main.cpp =================================================================== --- head/biology/ugene/files/patch-src_ugenecl_src_Main.cpp (revision 478817) +++ head/biology/ugene/files/patch-src_ugenecl_src_Main.cpp (revision 478818) @@ -1,32 +1,36 @@ ---- 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 #include #include -#include +//#include // 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) { +#if 0 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); - CrashHandler::shutdown(); + //CrashHandler::shutdown(); return rc; } Index: head/biology/ugene/files/patch-src_ugeneui_src_Main.cpp =================================================================== --- head/biology/ugene/files/patch-src_ugeneui_src_Main.cpp (revision 478817) +++ head/biology/ugene/files/patch-src_ugeneui_src_Main.cpp (revision 478818) @@ -1,32 +1,36 @@ ---- 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 #include #include -#include +//#include #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) { +#if 0 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(); - CrashHandler::shutdown(); + //CrashHandler::shutdown(); return rc; } Index: head/biology/ugene/files/patch-ugene.pro =================================================================== --- head/biology/ugene/files/patch-ugene.pro (revision 478817) +++ head/biology/ugene/files/patch-ugene.pro (revision 478818) @@ -1,28 +1,29 @@ ---- 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() { } SUBDIRS += \ - 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 #foreach 'language' for( i, UGENE_TRANSL_IDX ) { Index: head/biology/ugene/pkg-plist =================================================================== --- head/biology/ugene/pkg-plist (revision 478817) +++ head/biology/ugene/pkg-plist (revision 478818) @@ -1,1447 +1,1492 @@ 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 lib/ugene/libU2Algorithm.so.1.0.0 lib/ugene/libU2Core.so lib/ugene/libU2Core.so.1 lib/ugene/libU2Core.so.1.0 lib/ugene/libU2Core.so.1.0.0 lib/ugene/libU2Designer.so lib/ugene/libU2Designer.so.1 lib/ugene/libU2Designer.so.1.0 lib/ugene/libU2Designer.so.1.0.0 lib/ugene/libU2Formats.so lib/ugene/libU2Formats.so.1 lib/ugene/libU2Formats.so.1.0 lib/ugene/libU2Formats.so.1.0.0 lib/ugene/libU2Gui.so lib/ugene/libU2Gui.so.1 lib/ugene/libU2Gui.so.1.0 lib/ugene/libU2Gui.so.1.0.0 lib/ugene/libU2Lang.so lib/ugene/libU2Lang.so.1 lib/ugene/libU2Lang.so.1.0 lib/ugene/libU2Lang.so.1.0.0 lib/ugene/libU2Private.so lib/ugene/libU2Private.so.1 lib/ugene/libU2Private.so.1.0 lib/ugene/libU2Private.so.1.0.0 -lib/ugene/libU2Remote.so -lib/ugene/libU2Remote.so.1 -lib/ugene/libU2Remote.so.1.0 -lib/ugene/libU2Remote.so.1.0.0 lib/ugene/libU2Script.so lib/ugene/libU2Script.so.1 lib/ugene/libU2Script.so.1.0 lib/ugene/libU2Script.so.1.0.0 lib/ugene/libU2Test.so lib/ugene/libU2Test.so.1 lib/ugene/libU2Test.so.1.0 lib/ugene/libU2Test.so.1.0.0 lib/ugene/libU2View.so lib/ugene/libU2View.so.1 lib/ugene/libU2View.so.1.0 lib/ugene/libU2View.so.1.0.0 -lib/ugene/libgtest.so -lib/ugene/libgtest.so.1 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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 lib/ugene/plugins/libchroma_view.so.1.0.0 lib/ugene/plugins/libcircular_view.so lib/ugene/plugins/libcircular_view.so.1 lib/ugene/plugins/libcircular_view.so.1.0 lib/ugene/plugins/libcircular_view.so.1.0.0 +lib/ugene/plugins/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 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lib/ugene/plugins/opencl_support.plugin lib/ugene/plugins/orf_marker.license lib/ugene/plugins/orf_marker.plugin lib/ugene/plugins/pcr.license lib/ugene/plugins/pcr.plugin lib/ugene/plugins/perf_monitor.license lib/ugene/plugins/perf_monitor.plugin lib/ugene/plugins/phylip.license lib/ugene/plugins/phylip.plugin lib/ugene/plugins/primer3.license lib/ugene/plugins/primer3.plugin lib/ugene/plugins/psipred.license lib/ugene/plugins/psipred.plugin lib/ugene/plugins/ptools.license lib/ugene/plugins/ptools.plugin lib/ugene/plugins/query_designer.license 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 lib/ugene/plugins/sitecon.plugin lib/ugene/plugins/smith_waterman.license lib/ugene/plugins/smith_waterman.plugin 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%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hmx1_3423.1.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hmx2_3424.3.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hmx3_3490.2.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Homez_1063.2.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxa10_2318.1.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxa11_2218.1.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxa13_3126.1.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxa1_3425.1.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxa2_3079.1.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxa3_2783.2.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxa4_3426.1.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxa5_3415.1.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxa6_1040.1.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxa7_2668.2.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxa7_3750.1.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxa9_2622.2.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxb13_3479.1.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxb3_1720.2.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxb4_2627.1.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxb5_3122.2.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxb6_3428.2.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxb7_3953.1.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxb8_3780.2.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxb9_3413.1.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxc10_2779.2.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxc11_3718.2.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxc12_3480.1.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxc13_3127.1.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxc4_3491.1.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxc5_2630.2.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxc6_3954.2.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxc8_3429.2.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxc9_2367.2.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxd10_2368.2.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxd11_3873.1.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxd12_3481.1.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxd13_2356.1.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxd1_3448.1.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxd3_1742.2.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxd8_2644.1.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Ipf1_3815.1.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Irx2_0900.3.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Irx3_0920.1.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Irx3_2226.1.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Irx4_2242.3.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Irx5_2385.1.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Irx6_2623.2.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Isl2_3430.1.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Isx_3445.1.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Lbx2_3869.2.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Lhx1_2240.2.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Lhx2_0953.2.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Lhx3_3431.1.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Lhx4_1719.2.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Lhx5_2279.1.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Lhx6_2272.1.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Lhx6_3432.1.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Lhx8_2247.2.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Lhx9_3492.1.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Lmx1a_2238.2.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Lmx1b_3433.2.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Meis1_2335.1.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Meox1_2310.2.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Mrg1_2246.2.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Mrg2_2302.1.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Msx1_3031.2.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Msx2_3449.1.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Msx3_3206.1.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Nkx1-1_3856.3.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Nkx1-2_3214.1.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Nkx2-2_2823.1.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Nkx2-3_3435.1.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Nkx2-4_3074.1.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Nkx2-5_3436.1.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Nkx2-6_3437.1.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Nkx2-9_3082.1.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Nkx3-1_2923.2.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Nkx6-1_2825.1.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Nkx6-1_2825.2.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Nkx6-3_3446.1.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Obox1_3970.2.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Obox2_3438.2.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Obox3_3439.1.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Obox5_2284.1.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Obox5_3963.2.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Obox6_3440.2.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Og2x_3719.1.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Otp_3496.1.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Otx1_2325.1.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Otx2_3441.1.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Pax4_3989.2.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Pax6_3838.3.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Pax7_3783.1.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Pbx1_3203.1.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Phox2a_3947.1.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Phox2b_3948.1.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Pitx1_2312.1.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Pitx2_2274.3.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Pitx3_3497.2.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Pknox1_2364.2.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Pknox2_3077.2.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Pou1f1_3818.1.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Pou2f1_3081.2.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Pou2f2_3748.1.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Pou2f3_3986.2.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Pou3f1_3819.1.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Pou3f2_2824.1.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Pou3f3_3235.2.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Pou3f4_3773.1.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Pou4f3_2791.1.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Pou6f1_1731.2.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Pou6f1_3733.1.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Prop1_3949.1.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Prrx1_3442.1.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Prrx2_3072.1.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Rax_3443.1.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Rhox11_1765.2.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Rhox11_2205.1.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Rhox6_4251.1.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Shox2_2641.2.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Six1_0935.2.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Six2_2307.2.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Six3_1732.2.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Six4_2860.1.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Six6_2267.4.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Six6_2267.5.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Tcf1_2666.2.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Tcf2_0913.2.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Tgif1_2342.2.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Tgif2_3451.1.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Titf1_1722.2.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Tlx2_3498.2.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Uncx4.1_2281.2.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Vax1_3499.1.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Vax2_3500.1.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Vsx1_1728.1.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Aft1.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Aro80.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Asg1.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Bas1.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Cbf1.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Cep3.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Cha4.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Cup9.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Ecm22.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Fhl1.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Fkh1.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Fkh2.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Gal4.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Gat1.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Gat3.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Gat4.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Gcn4.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Gln3.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Gsm1.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Gzf3.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Hal9.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Leu3.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Lys14.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Matalpha2.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Mbp1.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Mcm1.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Met32.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Mga1.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Mig1.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Mig2.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Mig3.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Ndt80.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Nhp6a.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Nhp6b.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Nrg1.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Oaf1.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Pbf1.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Pbf2.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Pdr1.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Phd1.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Pho2.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Pho4.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Put3.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Rap1.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Rdr1.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Rds1.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Rds2.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Rgt1.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Rph1.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Rpn4.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Rsc3.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Rsc30.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Rtg3.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Sfl1.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Sfp1.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Sip4.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Skn7.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Smp1.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Spt15.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Srd1.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Stb3.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Stp2.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Stp4.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Sum1.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Sut2.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Tbf1.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Tbs1.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Tea1.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Tec1.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Tye7.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Ume6.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Usv1.pwm %%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Xbp1.pwm 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