Date: Sun, 2 Sep 2018 20:47:15 +0000 (UTC) From: "Jason E. Hale" <jhale@FreeBSD.org> To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r478818 - in head/biology/ugene: . files Message-ID: <201809022047.w82KlF1p020281@repo.freebsd.org>
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Author: jhale Date: Sun Sep 2 20:47:15 2018 New Revision: 478818 URL: https://svnweb.freebsd.org/changeset/ports/478818 Log: Update to 1.31.0 PR: 229463 Approved by: Hannes Hauswedell <h2+fbsdports@fsfe.org> (maintainer) Added: head/biology/ugene/files/patch-git_578c949 (contents, props changed) head/biology/ugene/files/patch-src_libs__3rdparty_QSpec_src_drivers_GTKeyboardDriverLinux.cpp (contents, props changed) head/biology/ugene/files/patch-src_libs__3rdparty_QSpec_src_drivers_GTMouseDriverLinux.cpp (contents, props changed) Deleted: head/biology/ugene/files/patch-git_279756e4 head/biology/ugene/files/patch-src_libs__3rdparty_samtools_samtools.pri head/biology/ugene/files/patch-src_plugins__3rdparty_phylip_src_phylip.h head/biology/ugene/files/patch-src_plugins__3rdparty_umuscle_src_MuscleWorkPool.cpp head/biology/ugene/files/patch-src_plugins__3rdparty_variants_variants.pri head/biology/ugene/files/patch-src_ugene__globals.pri Modified: head/biology/ugene/Makefile head/biology/ugene/distinfo head/biology/ugene/files/patch-src_corelibs_U2Private_U2Private.pro head/biology/ugene/files/patch-src_plugins__checker_src_Main.cpp head/biology/ugene/files/patch-src_ugenecl_src_Main.cpp head/biology/ugene/files/patch-src_ugeneui_src_Main.cpp head/biology/ugene/files/patch-ugene.pro head/biology/ugene/pkg-plist Modified: head/biology/ugene/Makefile ============================================================================== --- head/biology/ugene/Makefile Sun Sep 2 20:30:45 2018 (r478817) +++ head/biology/ugene/Makefile Sun Sep 2 20:47:15 2018 (r478818) @@ -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 \ @@ -14,46 +13,42 @@ 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 <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 @@ post-patch: ${WRKSRC}/installer/_common_data/ugene @${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 \ Modified: head/biology/ugene/distinfo ============================================================================== --- head/biology/ugene/distinfo Sun Sep 2 20:30:45 2018 (r478817) +++ head/biology/ugene/distinfo Sun Sep 2 20:47:15 2018 (r478818) @@ -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 Added: head/biology/ugene/files/patch-git_578c949 ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/ugene/files/patch-git_578c949 Sun Sep 2 20:47:15 2018 (r478818) @@ -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" Modified: head/biology/ugene/files/patch-src_corelibs_U2Private_U2Private.pro ============================================================================== --- head/biology/ugene/files/patch-src_corelibs_U2Private_U2Private.pro Sun Sep 2 20:30:45 2018 (r478817) +++ head/biology/ugene/files/patch-src_corelibs_U2Private_U2Private.pro Sun Sep 2 20:47:15 2018 (r478818) @@ -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 { Added: head/biology/ugene/files/patch-src_libs__3rdparty_QSpec_src_drivers_GTKeyboardDriverLinux.cpp ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/ugene/files/patch-src_libs__3rdparty_QSpec_src_drivers_GTKeyboardDriverLinux.cpp Sun Sep 2 20:47:15 2018 (r478818) @@ -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" + Added: head/biology/ugene/files/patch-src_libs__3rdparty_QSpec_src_drivers_GTMouseDriverLinux.cpp ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/ugene/files/patch-src_libs__3rdparty_QSpec_src_drivers_GTMouseDriverLinux.cpp Sun Sep 2 20:47:15 2018 (r478818) @@ -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); Modified: head/biology/ugene/files/patch-src_plugins__checker_src_Main.cpp ============================================================================== --- head/biology/ugene/files/patch-src_plugins__checker_src_Main.cpp Sun Sep 2 20:30:45 2018 (r478817) +++ head/biology/ugene/files/patch-src_plugins__checker_src_Main.cpp Sun Sep 2 20:47:15 2018 (r478818) @@ -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); Modified: head/biology/ugene/files/patch-src_ugenecl_src_Main.cpp ============================================================================== --- head/biology/ugene/files/patch-src_ugenecl_src_Main.cpp Sun Sep 2 20:30:45 2018 (r478817) +++ head/biology/ugene/files/patch-src_ugenecl_src_Main.cpp Sun Sep 2 20:47:15 2018 (r478818) @@ -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); Modified: head/biology/ugene/files/patch-src_ugeneui_src_Main.cpp ============================================================================== --- head/biology/ugene/files/patch-src_ugeneui_src_Main.cpp Sun Sep 2 20:30:45 2018 (r478817) +++ head/biology/ugene/files/patch-src_ugeneui_src_Main.cpp Sun Sep 2 20:47:15 2018 (r478818) @@ -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(); Modified: head/biology/ugene/files/patch-ugene.pro ============================================================================== --- head/biology/ugene/files/patch-ugene.pro Sun Sep 2 20:30:45 2018 (r478817) +++ head/biology/ugene/files/patch-ugene.pro Sun Sep 2 20:47:15 2018 (r478818) @@ -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 Modified: head/biology/ugene/pkg-plist ============================================================================== --- head/biology/ugene/pkg-plist Sun Sep 2 20:30:45 2018 (r478817) +++ head/biology/ugene/pkg-plist Sun Sep 2 20:47:15 2018 (r478818) @@ -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 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 @@ -43,16 +43,14 @@ 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 -lib/ugene/libgtest.so.1.0 -lib/ugene/libgtest.so.1.0.0 lib/ugene/libugenedb.so lib/ugene/libugenedb.so.1 lib/ugene/libugenedb.so.1.0 lib/ugene/libugenedb.so.1.0.0 lib/ugene/plugins/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.license 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.license lib/ugene/plugins/gor4.plugin lib/ugene/plugins/hmm2.license lib/ugene/plugins/hmm2.plugin -%%SSE2%%lib/ugene/plugins/hmm3.license -%%SSE2%%lib/ugene/plugins/hmm3.plugin lib/ugene/plugins/kalign.license lib/ugene/plugins/kalign.plugin +lib/ugene/plugins/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 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 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 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 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 @@ -253,12 +267,18 @@ lib/ugene/plugins/libweight_matrix.so 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 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.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 @@ -289,12 +307,14 @@ lib/ugene/plugins/smith_waterman.license 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/ugenem 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 @@ share/pixmaps/ugene.xpm %%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 @@ share/pixmaps/ugene.xpm %%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 @@ share/pixmaps/ugene.xpm %%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 @@ share/pixmaps/ugene.xpm %%DATADIR%%/workflow_samples/Data merging/tfbs.uwl %%DATADIR%%/workflow_samples/HMMER/build-test-HMM.uwl %%DATADIR%%/workflow_samples/HMMER/searchHMM.uwl -%%DATADIR%%/workflow_samples/NGS/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 @@ share/pixmaps/ugene.xpm %%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 @@ share/pixmaps/ugene.xpm %%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 @@ share/pixmaps/ugene.xpm %%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
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