git: 7f73f34aa06d - main - biology/ugene: Update to 53.1
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Date: Sat, 18 Apr 2026 20:44:19 UTC
The branch main has been updated by makc:
URL: https://cgit.FreeBSD.org/ports/commit/?id=7f73f34aa06d2c12fc03476b05ef8658c97b6989
commit 7f73f34aa06d2c12fc03476b05ef8658c97b6989
Author: Max Brazhnikov <makc@FreeBSD.org>
AuthorDate: 2026-04-18 20:44:01 +0000
Commit: Max Brazhnikov <makc@FreeBSD.org>
CommitDate: 2026-04-18 20:44:01 +0000
biology/ugene: Update to 53.1
Release Notes: https://ugene.net/changelist.html
Port changes:
- Fix build on non-x86, mark IGNORE for aarch64.
- Switch to cmake, qmake is not supported anymore.
- Drop unused sqlite, renew Qt components.
- Convert to PORTDATA, use shebangfix.
Special thanks to fuz@ for testing and fixing non-x86 build!
PR: 293379
---
biology/ugene/Makefile | 85 +-
biology/ugene/distinfo | 6 +-
biology/ugene/files/patch-linux | 42 +
biology/ugene/files/patch-qmutex | 64 ++
.../patch-src_corelibs_U2Private_U2Private.pro | 41 -
...rty_QSpec_src_drivers_GTKeyboardDriverLinux.cpp | 21 -
...dparty_QSpec_src_drivers_GTMouseDriverLinux.cpp | 20 -
.../ugene/files/patch-src_plugins__3rdparty_ball | 28 +
.../files/patch-src_plugins__checker_src_Main.cpp | 31 -
biology/ugene/files/patch-src_ugenecl_src_Main.cpp | 46 +-
biology/ugene/files/patch-src_ugeneui_src_Main.cpp | 45 -
biology/ugene/files/patch-sse2neon | 40 +
biology/ugene/files/patch-ugene.pro | 10 -
biology/ugene/files/patch-unix | 37 +
biology/ugene/pkg-plist | 1208 +-------------------
15 files changed, 297 insertions(+), 1427 deletions(-)
diff --git a/biology/ugene/Makefile b/biology/ugene/Makefile
index 959569de56f9..60d26dd34b52 100644
--- a/biology/ugene/Makefile
+++ b/biology/ugene/Makefile
@@ -1,6 +1,5 @@
PORTNAME= ugene
-PORTVERSION= 40.1
-PORTREVISION= 1
+PORTVERSION= 53.1
CATEGORIES= biology science
MAINTAINER= makc@FreeBSD.org
@@ -10,56 +9,72 @@ WWW= https://ugene.net/
LICENSE= GPLv2+
LICENSE_FILE= ${WRKSRC}/LICENSE.txt
-BROKEN_aarch64= fails to build: invokes x86 asm
-BROKEN_armv7= fails to build: src/SendReportDialog.cpp:435:20: error: invalid output constraint '=a' in asm, see https://github.com/ugeneunipro/ugene/issues/919
-BROKEN_riscv64= fails to build: invokes x86 asm
+IGNORE_aarch64= fails to build: https://bugs.freebsd.org/293379
RUN_DEPENDS= bash:shells/bash
-USE_GITHUB= yes
-GH_ACCOUNT= ugeneunipro
-
-USES= desktop-file-utils gl qmake qt:5 shared-mime-info sqlite xorg
+USES= cmake compiler:c++14-lang desktop-file-utils gl \
+ localbase:ldflags qt:5 shared-mime-info shebangfix xorg
USE_GL= gl glu
-USE_QT= buildtools:build linguisttools:build \
- core gui network opengl printsupport scripttools script \
- sql svg testlib widgets xml \
+USE_QT= buildtools:build linguisttools:build qmake:build \
+ core gui network networkauth printsupport \
+ svg testlib websockets widgets xml \
imageformats:run
USE_XORG= x11 xtst
+USE_LDCONFIG= ${UGENE_LIBDIR}
-QMAKE_ARGS= INSTALL_PREFIX="${PREFIX}" UGENE_INSTALL_DATA="${DATADIR}" \
- INSTALL_MANDIR="${PREFIX}/share/man" \
- UGENE_LRELEASE="${LRELEASE}" UGENE_LUPDATE="${LUPDATE}" \
- UGENE_USE_BUNDLED_SQLITE=0
-ALL_TARGET= release
-CXXFLAGS_i386= -msse2
+USE_GITHUB= yes
+GH_ACCOUNT= ugeneunipro
-OPTIONS_DEFINE= OPENCL
+CXXFLAGS_i386= -msse2
+LDFLAGS+= -pthread
+SHEBANG_FILES= etc/shared/ugene
+PORTDATA= *
-OPENCL_QMAKE_ON= UGENE_OPENCL_DETECTED=1
+UGENE_LIBDIR= ${PREFIX}/lib/ugene
.include <bsd.port.pre.mk>
-.if ${ARCH} == i386
-QMAKE_ARGS+= CONFIG+=x86
+.if empty(ARCH:Mamd64) && empty(ARCH:Mi386)
+BUILD_DEPENDS+= ${LOCALBASE}/include/sse2neon.h:devel/sse2neon
.endif
post-patch:
-# yes, bash is required, stuff will not execute with sh
- @${REINPLACE_CMD} -e 's|/bin/bash|/usr/bin/env bash|' \
- ${WRKSRC}/src/gen_bin_script.cmd \
- ${WRKSRC}/etc/shared/ugene ${WRKSRC}/etc/shared/ugened
@${REINPLACE_CMD} -e 's|-bit version|& for ${OPSYS}/${ARCH}|' \
${WRKSRC}/src/ugeneui/src/main_window/AboutDialogController.cpp
- @${REINPLACE_CMD} 's, -lbreakpad$$$$D,,' \
- ${WRKSRC}/src/corelibs/U2Private/U2Private.pri \
- ${WRKSRC}/src/plugins_checker/plugins_checker.pri \
- ${WRKSRC}/src/ugenecl/ugenecl.pri \
- ${WRKSRC}/src/ugeneui/ugeneui.pri
- @${REINPLACE_CMD} -e '/ugene\.desktop/s,share,&d,' \
- ${WRKSRC}/ugene.pri
+ ${REINPLACE_CMD} 's,stdc++fs,,' \
+ ${WRKSRC}/src/libs_3rdparty/QSpec/CMakeLists.txt
+ ${REINPLACE_CMD} 's,/usr/local/share/ugene,${DATADIR},' \
+ ${WRKSRC}/src/ugenecl/src/Main.cpp
+# breakpad is not aware of FreeBSD
+ ${REINPLACE_CMD} '/libs_3rdparty\/breakpad/d' \
+ ${WRKSRC}/src/corelibs/U2Private/CMakeLists.txt \
+ ${WRKSRC}/CMakeLists.txt
+ ${REINPLACE_CMD} 's,breakpad,,' \
+ ${WRKSRC}/src/ugeneui/CMakeLists.txt \
+ ${WRKSRC}/src/ugenecl/CMakeLists.txt \
+ ${WRKSRC}/src/corelibs/U2Private/CMakeLists.txt
+# Do not alter binary names for debug build
+ ${REINPLACE_CMD} '/DEBUG_POSTFIX/d' \
+ ${WRKSRC}/src/plugins_checker/CMakeLists.txt \
+ ${WRKSRC}/src/ugenecl/CMakeLists.txt \
+ ${WRKSRC}/src/ugenem/CMakeLists.txt \
+ ${WRKSRC}/src/ugeneui/CMakeLists.txt \
+ ${WRKSRC}/CMakeLists.txt
-post-stage:
- @cd ${STAGEDIR}${PREFIX} && ${RM} bin/ecp.* lib/ugene/ecp.*
+do-install:
+ ${MKDIR} ${STAGEDIR}/${UGENE_LIBDIR}
+ cd ${BUILD_WRKSRC}/dist && ${COPYTREE_SHARE} . ${STAGEDIR}/${UGENE_LIBDIR}/
+.for prog in ugene ugenecl ugenem ugeneui
+ ${RLN} ${STAGEDIR}${UGENE_LIBDIR}/${prog} ${STAGEDIR}/${PREFIX}/bin/${prog}
+.endfor
+ ${MKDIR} ${STAGEDIR}/${DATADIR}
+ cd ${WRKSRC} && ${COPYTREE_SHARE} data ${STAGEDIR}/${DATADIR}
+ ${INSTALL_DATA} ${WRKSRC}/etc/shared/ugene.desktop ${STAGEDIR}/${DESKTOPDIR}
+ ${INSTALL_DATA} ${WRKSRC}/etc/shared/ugene.png ${STAGEDIR}/${PREFIX}/share/pixmaps/
+ ${INSTALL_DATA} ${WRKSRC}/etc/shared/application-x-ugene-ext.png ${STAGEDIR}/${PREFIX}/share/pixmaps/
+ ${INSTALL_DATA} ${WRKSRC}/etc/shared/ugene.1.gz ${STAGEDIR}/${PREFIX}/share/man/man1/
+ ${MKDIR} ${STAGEDIR}/${PREFIX}/share/mime/packages
+ ${INSTALL_DATA} ${WRKSRC}/etc/shared/application-x-ugene.xml ${STAGEDIR}/${PREFIX}/share/mime/packages/
.include <bsd.port.post.mk>
diff --git a/biology/ugene/distinfo b/biology/ugene/distinfo
index 5eff6f289b9d..3d5da3ede80d 100644
--- a/biology/ugene/distinfo
+++ b/biology/ugene/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1633934483
-SHA256 (ugeneunipro-ugene-40.1_GH0.tar.gz) = 92b954449f697957c6b6b2da803ba6ae9ad546f44c584bbb2ab8600ac8b45a6e
-SIZE (ugeneunipro-ugene-40.1_GH0.tar.gz) = 28791083
+TIMESTAMP = 1775033524
+SHA256 (ugeneunipro-ugene-53.1_GH0.tar.gz) = 3eca3bc97824d855b5dfe4844b7a5d46052f98279fa015c7e152e111f89c4673
+SIZE (ugeneunipro-ugene-53.1_GH0.tar.gz) = 27484438
diff --git a/biology/ugene/files/patch-linux b/biology/ugene/files/patch-linux
new file mode 100644
index 000000000000..f334ee07eca0
--- /dev/null
+++ b/biology/ugene/files/patch-linux
@@ -0,0 +1,42 @@
+--- src/corelibs/U2Private/src/crash_handler/CrashHandler.cpp.orig 2026-03-01 18:44:47 UTC
++++ src/corelibs/U2Private/src/crash_handler/CrashHandler.cpp
+@@ -36,7 +36,7 @@
+
+ #if defined(Q_OS_DARWIN)
+ # include "CrashHandlerPrivateMac.h"
+-#elif defined(Q_OS_UNIX) && !defined(Q_OS_DARWIN)
++#elif defined(Q_OS_LINUX)
+ # include "CrashHandlerPrivateUnixNotMac.h"
+ #elif defined(Q_OS_WIN)
+ # include "CrashHandlerPrivateWin.h"
+@@ -124,7 +124,7 @@ void CrashHandler::setupPrivateHandler() {
+ assert(crashHandlerPrivate == nullptr);
+ #if defined(Q_OS_DARWIN)
+ crashHandlerPrivate = new CrashHandlerPrivateMac;
+-#elif defined(Q_OS_UNIX) && !defined(Q_OS_DARWIN)
++#elif defined(Q_OS_LINUX)
+ crashHandlerPrivate = new CrashHandlerPrivateUnixNotMac;
+ #elif defined(Q_OS_WIN)
+ crashHandlerPrivate = new CrashHandlerPrivateWin;
+--- src/corelibs/U2Private/src/crash_handler/CrashHandlerPrivateUnixNotMac.cpp.orig 2026-03-01 18:44:47 UTC
++++ src/corelibs/U2Private/src/crash_handler/CrashHandlerPrivateUnixNotMac.cpp
+@@ -20,7 +20,7 @@
+ */
+
+ #include <qglobal.h>
+-#if defined(Q_OS_UNIX) && !defined(Q_OS_DARWIN)
++#if defined(Q_OS_LINUX)
+
+ # include <execinfo.h>
+
+--- src/corelibs/U2Private/src/crash_handler/CrashHandlerPrivateUnixNotMac.h.orig 2026-03-01 18:44:47 UTC
++++ src/corelibs/U2Private/src/crash_handler/CrashHandlerPrivateUnixNotMac.h
+@@ -22,7 +22,7 @@
+ #pragma once
+
+ #include <qglobal.h>
+-#if defined(Q_OS_UNIX) && !defined(Q_OS_DARWIN)
++#if defined(Q_OS_LINUX)
+
+ # include <client/linux/handler/exception_handler.h>
+
diff --git a/biology/ugene/files/patch-qmutex b/biology/ugene/files/patch-qmutex
new file mode 100644
index 000000000000..a11b98d3fce2
--- /dev/null
+++ b/biology/ugene/files/patch-qmutex
@@ -0,0 +1,64 @@
+--- src/corelibs/U2Algorithm/src/registry/SubstMatrixRegistry.cpp.orig 2026-03-01 18:44:47 UTC
++++ src/corelibs/U2Algorithm/src/registry/SubstMatrixRegistry.cpp
+@@ -30,7 +30,7 @@ SubstMatrixRegistry::SubstMatrixRegistry(QObject* pOwn
+ namespace U2 {
+
+ SubstMatrixRegistry::SubstMatrixRegistry(QObject* pOwn)
+- : QObject(pOwn), mutex(QMutex::Recursive) {
++ : QObject(pOwn), mutex() {
+ readMatrices();
+ }
+
+--- src/corelibs/U2Algorithm/src/registry/SubstMatrixRegistry.h.orig 2026-03-01 18:44:47 UTC
++++ src/corelibs/U2Algorithm/src/registry/SubstMatrixRegistry.h
+@@ -53,7 +53,7 @@ class U2ALGORITHM_EXPORT SubstMatrixRegistry : public
+ void readMatrices();
+ static SMatrix parseMatrix(const QString& name, const QByteArray& text, QString& error);
+
+- mutable QMutex mutex;
++ mutable QRecursiveMutex mutex;
+ QMap<QString, SMatrix> matrixByName;
+ };
+
+--- src/plugins/annotator/src/CollocationsDialogController.cpp.orig 2026-03-01 18:44:47 UTC
++++ src/plugins/annotator/src/CollocationsDialogController.cpp
+@@ -313,7 +313,7 @@ CollocationSearchTask::CollocationSearchTask(const QLi
+ //////////////////////////////////////////////////////////////////////////
+ // task
+ CollocationSearchTask::CollocationSearchTask(const QList<AnnotationTableObject*>& table, const QSet<QString>& names, const CollocationsAlgorithmSettings& cfg)
+- : Task(tr("Search for annotated regions"), TaskFlag_None), cfg(cfg), lock(QMutex::Recursive), keepSourceAnns(false) {
++ : Task(tr("Search for annotated regions"), TaskFlag_None), cfg(cfg), lock(), keepSourceAnns(false) {
+ GCOUNTER(cvar, "CollocationSearchTask");
+ assert(cfg.distance >= 0);
+ assert(!names.isEmpty());
+@@ -342,7 +342,7 @@ CollocationSearchTask::CollocationSearchTask(const QLi
+ }
+
+ CollocationSearchTask::CollocationSearchTask(const QList<SharedAnnotationData>& table, const QSet<QString>& names, const CollocationsAlgorithmSettings& cfg, bool _keepSourceAnns)
+- : Task(tr("Search for annotated regions"), TaskFlag_None), cfg(cfg), lock(QMutex::Recursive), keepSourceAnns(_keepSourceAnns) {
++ : Task(tr("Search for annotated regions"), TaskFlag_None), cfg(cfg), lock(), keepSourceAnns(_keepSourceAnns) {
+ assert(cfg.distance >= 0);
+ assert(!names.isEmpty());
+ foreach (const QString& name, names) {
+--- src/plugins/annotator/src/CollocationsDialogController.h.orig 2026-03-01 18:44:47 UTC
++++ src/plugins/annotator/src/CollocationsDialogController.h
+@@ -105,7 +105,7 @@ class CollocationSearchTask : public Task, public Coll
+ QMap<QString, CollocationsAlgorithmItem> items;
+ CollocationsAlgorithmSettings cfg;
+ QVector<U2Region> results;
+- QMutex lock;
++ QRecursiveMutex lock;
+
+ const bool keepSourceAnns;
+ QList<SharedAnnotationData> sourceAnns;
+--- src/plugins/dna_export/src/ExportSequenceTask.cpp.orig 2026-03-01 18:44:47 UTC
++++ src/plugins/dna_export/src/ExportSequenceTask.cpp
+@@ -46,7 +46,7 @@ static const qint64 MAX_CHUNK_LENGTH = 4194305; // (4
+
+ static const qint64 MAX_CHUNK_LENGTH = 4194305; // (4 MiB + 1) chunk. Remainder of the division by 3 is 2.
+
+-static QMutex seqRefGuard(QMutex::NonRecursive);
++static QMutex seqRefGuard;
+
+ namespace U2 {
+
diff --git a/biology/ugene/files/patch-src_corelibs_U2Private_U2Private.pro b/biology/ugene/files/patch-src_corelibs_U2Private_U2Private.pro
deleted file mode 100644
index 73f2d4038887..000000000000
--- a/biology/ugene/files/patch-src_corelibs_U2Private_U2Private.pro
+++ /dev/null
@@ -1,41 +0,0 @@
---- 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 \
-@@ -30,23 +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/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 {
diff --git a/biology/ugene/files/patch-src_libs__3rdparty_QSpec_src_drivers_GTKeyboardDriverLinux.cpp b/biology/ugene/files/patch-src_libs__3rdparty_QSpec_src_drivers_GTKeyboardDriverLinux.cpp
deleted file mode 100644
index c6956606c3ed..000000000000
--- a/biology/ugene/files/patch-src_libs__3rdparty_QSpec_src_drivers_GTKeyboardDriverLinux.cpp
+++ /dev/null
@@ -1,21 +0,0 @@
-Use the Linux driver for FreeBSD as well. Fixes crash on startup.
-
---- src/libs_3rdparty/QSpec/src/drivers/GTKeyboardDriverLinux.cpp.orig 2021-09-08 14:18:53 UTC
-+++ src/libs_3rdparty/QSpec/src/drivers/GTKeyboardDriverLinux.cpp
-@@ -21,14 +21,14 @@
-
- #include "GTKeyboardDriver.h"
-
--#if defined __linux__
-+#if defined(__linux__) || defined(__FreeBSD__)
- # include <X11/extensions/XTest.h>
- # include <X11/keysym.h>
- #endif
-
- namespace HI {
-
--#if defined __linux__
-+#if defined(__linux__) || defined(__FreeBSD__)
-
- bool GTKeyboardDriver::keyPress(char key, Qt::KeyboardModifiers modifiers) {
- DRIVER_CHECK(key != 0, "key = 0");
diff --git a/biology/ugene/files/patch-src_libs__3rdparty_QSpec_src_drivers_GTMouseDriverLinux.cpp b/biology/ugene/files/patch-src_libs__3rdparty_QSpec_src_drivers_GTMouseDriverLinux.cpp
deleted file mode 100644
index eb0c977bf399..000000000000
--- a/biology/ugene/files/patch-src_libs__3rdparty_QSpec_src_drivers_GTMouseDriverLinux.cpp
+++ /dev/null
@@ -1,20 +0,0 @@
-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
-@@ -23,13 +23,13 @@
-
- #include "GTMouseDriver.h"
-
--#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);
diff --git a/biology/ugene/files/patch-src_plugins__3rdparty_ball b/biology/ugene/files/patch-src_plugins__3rdparty_ball
new file mode 100644
index 000000000000..762c43a53506
--- /dev/null
+++ b/biology/ugene/files/patch-src_plugins__3rdparty_ball
@@ -0,0 +1,28 @@
+Description: indicating we use signed char, so that we don't depend on the
+ default choice of the implementation
+Author: Pierre Gruet <pgt@debian.org>
+Forwarded: no
+Last-Update: 2024-10-04
+
+--- src/plugins_3rdparty/ball/src/include/BALL/DATATYPE/hashGrid.h
++++ src/plugins_3rdparty/ball/src/include/BALL/DATATYPE/hashGrid.h
+@@ -37,7 +37,7 @@
+ {
+ namespace __private
+ {
+- extern const char BALL_EXPORT neighbour_table_[27][3];
++ extern const signed char BALL_EXPORT neighbour_table_[27][3];
+ }
+
+ template <typename Item> class HashGrid3;
+--- src/plugins_3rdparty/ball/src/source/DATATYPE/hashGrid.cpp
++++ src/plugins_3rdparty/ball/src/source/DATATYPE/hashGrid.cpp
+@@ -9,7 +9,7 @@
+ {
+ namespace __private
+ {
+- const char neighbour_table_[27][3] =
++ const signed char neighbour_table_[27][3] =
+ {
+ { 0, 0, 0 }, { 0, 0, -1 }, { 0, 0, 1 },
+ { 0, -1, -1 }, { 0, -1, 0 }, { 0, -1, 1 },
diff --git a/biology/ugene/files/patch-src_plugins__checker_src_Main.cpp b/biology/ugene/files/patch-src_plugins__checker_src_Main.cpp
deleted file mode 100644
index e893985f32c3..000000000000
--- a/biology/ugene/files/patch-src_plugins__checker_src_Main.cpp
+++ /dev/null
@@ -1,31 +0,0 @@
---- 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>
- #include <SettingsImpl.h>
- #include <TaskSchedulerImpl.h>
--#include <crash_handler/CrashHandler.h>
-+//#include <crash_handler/CrashHandler.h>
-
- #define TR_SETTINGS_ROOT QString("test_runner/")
-
-@@ -55,8 +55,10 @@ static void registerCoreServices() {
- }
- #endif
-
-+#if 0
- CrashHandler::setupHandler();
- CrashHandler::setSendCrashReports(false);
-+#endif
-
- const char* build = QT_VERSION_STR, *runtime = qVersion();
- if (strcmp(build, runtime) > 0){
-@@ -141,7 +143,7 @@ int main(int argc, char **argv)
- delete cmdLineRegistry;
- appContext->setCMDLineRegistry(NULL);
-
-- CrashHandler::shutdown();
-+ //CrashHandler::shutdown();
-
- return rc;
- }
diff --git a/biology/ugene/files/patch-src_ugenecl_src_Main.cpp b/biology/ugene/files/patch-src_ugenecl_src_Main.cpp
index 1e91ae0651d0..b14f4f39b5f1 100644
--- a/biology/ugene/files/patch-src_ugenecl_src_Main.cpp
+++ b/biology/ugene/files/patch-src_ugenecl_src_Main.cpp
@@ -1,36 +1,20 @@
---- src/ugenecl/src/Main.cpp.orig 2018-08-16 13:59:20 UTC
+--- src/ugenecl/src/Main.cpp.orig 2026-03-01 18:44:47 UTC
+++ src/ugenecl/src/Main.cpp
-@@ -93,7 +93,7 @@
- #include <ServiceRegistryImpl.h>
- #include <SettingsImpl.h>
- #include <TaskSchedulerImpl.h>
--#include <crash_handler/CrashHandler.h>
-+//#include <crash_handler/CrashHandler.h>
-
- // local project imports
- #include "DumpHelpTask.h"
-@@ -191,6 +191,7 @@ static void setSearchPaths() {
- }
-
- int main(int argc, char **argv) {
-+#if 0
- if (CrashHandler::isEnabled()) {
- CrashHandler::setupHandler();
+@@ -151,7 +151,7 @@ static void setScriptsSearchPath() {
+ scriptsSearchPath.push_back(appDirPath + RELATIVE_DEV_SCRIPTS_DIR);
}
-@@ -198,6 +199,7 @@ int main(int argc, char **argv)
- if (qgetenv(ENV_SEND_CRASH_REPORTS) == "0") {
- CrashHandler::setSendCrashReports(false);
+ if (scriptsSearchPath.empty()) {
+- scriptsSearchPath.push_back("/");
++ scriptsSearchPath.push_back("/usr/local/share/ugene/scripts");
+ }
+ QDir::setSearchPaths(PATH_PREFIX_SCRIPTS, scriptsSearchPath);
+ }
+@@ -178,7 +178,7 @@ static void setDataSearchPaths() {
}
-+#endif
-
- if (!Version::checkBuildAndRuntimeVersions()) {
- return -1;
-@@ -617,7 +619,7 @@ int main(int argc, char **argv)
- delete pwr;
- appContext->setAlignmentAlgorithmsRegistry(NULL);
-- CrashHandler::shutdown();
-+ //CrashHandler::shutdown();
+ if (dataSearchPaths.empty()) {
+- dataSearchPaths.push_back("/");
++ dataSearchPaths.push_back("/usr/local/share/ugene/data");
+ }
- return rc;
- }
+ QDir::setSearchPaths(PATH_PREFIX_DATA, dataSearchPaths);
diff --git a/biology/ugene/files/patch-src_ugeneui_src_Main.cpp b/biology/ugene/files/patch-src_ugeneui_src_Main.cpp
deleted file mode 100644
index 251f739fbf1e..000000000000
--- a/biology/ugene/files/patch-src_ugeneui_src_Main.cpp
+++ /dev/null
@@ -1,45 +0,0 @@
---- src/ugeneui/src/Main.cpp.orig 2020-06-17 15:14:26 UTC
-+++ src/ugeneui/src/Main.cpp
-@@ -151,7 +151,7 @@
- #include <ServiceRegistryImpl.h>
- #include <SettingsImpl.h>
- #include <TaskSchedulerImpl.h>
--#include <crash_handler/CrashHandler.h>
-+//#include <crash_handler/CrashHandler.h>
-
- #include "app_settings/AppSettingsGUIImpl.h"
- #include "app_settings/logview_settings/LogSettingsGUIController.h"
-@@ -403,6 +403,7 @@ void fixMacFonts() {
- } // namespace
-
- int main(int argc, char **argv) {
-+#if 0
- if (CrashHandler::isEnabled()) {
- CrashHandler::setupHandler();
- }
-@@ -410,6 +411,7 @@ 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);
-
-@@ -422,7 +424,7 @@ int main(int argc, char **argv) {
- //QApplication app(argc, argv);
- GApplication app(argc, argv);
-
--#ifdef Q_OS_LINUX
-+#ifdef Q_OS_UNIX
- QPixmap pixmap(":/ugene/images/originals/ugene_128.png");
- app.setWindowIcon(pixmap);
- #endif
-@@ -1088,7 +1090,7 @@ int main(int argc, char **argv) {
- }
-
- UgeneUpdater::onClose();
-- CrashHandler::shutdown();
-+ //CrashHandler::shutdown();
-
- return rc;
- }
diff --git a/biology/ugene/files/patch-sse2neon b/biology/ugene/files/patch-sse2neon
new file mode 100644
index 000000000000..145f1a34811e
--- /dev/null
+++ b/biology/ugene/files/patch-sse2neon
@@ -0,0 +1,40 @@
+--- src/plugins_3rdparty/hmm2/src/u_search/uhmmsearch_sse.cpp.orig 2026-03-01 18:44:47 UTC
++++ src/plugins_3rdparty/hmm2/src/u_search/uhmmsearch_sse.cpp
+@@ -1,5 +1,9 @@
+ #include <assert.h>
++#if defined(__i386__) || defined(__amd64__)
+ #include <emmintrin.h>
++#else
++#include <sse2neon.h>
++#endif
+ #include <hmmer2/funcs.h>
+
+ #include <U2Core/SequenceWalkerTask.h>
+--- src/plugins/smith_waterman/src/SmithWatermanAlgorithmSSE2.cpp.orig 2026-03-01 18:44:47 UTC
++++ src/plugins/smith_waterman/src/SmithWatermanAlgorithmSSE2.cpp
+@@ -23,7 +23,11 @@ U2_DISABLE_WARNINGS
+ * MA 02110-1301, USA.
+ */
+
++#if defined(__i386__) || defined(__amd64__)
+ #include <emmintrin.h>
++#else
++#include <sse2neon.h>
++#endif
+ #include <iostream>
+
+ #include "SmithWatermanAlgorithmSSE2.h"
+--- src/plugins/smith_waterman/src/SmithWatermanAlgorithmSSE2.h.orig 2026-03-01 18:44:47 UTC
++++ src/plugins/smith_waterman/src/SmithWatermanAlgorithmSSE2.h
+@@ -21,7 +21,11 @@
+
+ #pragma once
+
++#if defined(__i386__) || defined(__amd64__)
+ #include <emmintrin.h>
++#else
++#include <sse2neon.h>
++#endif
+
+ #include "SmithWatermanAlgorithm.h"
+
diff --git a/biology/ugene/files/patch-ugene.pro b/biology/ugene/files/patch-ugene.pro
deleted file mode 100644
index 29854f16d39d..000000000000
--- a/biology/ugene/files/patch-ugene.pro
+++ /dev/null
@@ -1,10 +0,0 @@
---- 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/samtools \
diff --git a/biology/ugene/files/patch-unix b/biology/ugene/files/patch-unix
new file mode 100644
index 000000000000..f230ec9ff5d5
--- /dev/null
+++ b/biology/ugene/files/patch-unix
@@ -0,0 +1,37 @@
+--- src/libs_3rdparty/QSpec/src/drivers/GTKeyboardDriverLinux.cpp.orig 2026-03-01 18:44:47 UTC
++++ src/libs_3rdparty/QSpec/src/drivers/GTKeyboardDriverLinux.cpp
+@@ -21,14 +21,14 @@
+
+ #include "GTKeyboardDriver.h"
+
+-#if defined __linux__
++#if defined(Q_OS_UNIX)
+ # include <X11/extensions/XTest.h>
+ # include <X11/keysym.h>
+ #endif
+
+ namespace HI {
+
+-#if defined __linux__
++#if defined(Q_OS_UNIX)
+
+ void GTKeyboardDriver::releasePressedKeys() {
+ GTKeyboardDriver::keyRelease(Qt::Key_Control);
+--- src/libs_3rdparty/QSpec/src/drivers/GTMouseDriverLinux.cpp.orig 2026-03-01 18:44:47 UTC
++++ src/libs_3rdparty/QSpec/src/drivers/GTMouseDriverLinux.cpp
+@@ -24,13 +24,13 @@
+ #include <QByteArray>
+
+ #include "GTMouseDriver.h"
+-#ifdef __linux__
++#ifdef Q_OS_UNIX
+ # include <X11/extensions/XTest.h>
+ #endif
+
+ namespace HI {
+
+-#ifdef __linux__
++#ifdef Q_OS_UNIX
+
+ # define DELAY_ON_EVERY_N_PX 16
+ /**
diff --git a/biology/ugene/pkg-plist b/biology/ugene/pkg-plist
index 10133c926025..028dd4d78d49 100644
--- a/biology/ugene/pkg-plist
+++ b/biology/ugene/pkg-plist
@@ -1,4 +1,7 @@
bin/ugene
+bin/ugenecl
+bin/ugenem
+bin/ugeneui
lib/ugene/libQSpec.so
lib/ugene/libU2Algorithm.so
lib/ugene/libU2Core.so
@@ -10,6 +13,11 @@ lib/ugene/libU2Private.so
lib/ugene/libU2Script.so
lib/ugene/libU2Test.so
lib/ugene/libU2View.so
+lib/ugene/libqscore.a
+lib/ugene/libqtscript.so
+lib/ugene/libsamtools.a
+lib/ugene/libugenedb.so
+lib/ugene/libzlib.a
lib/ugene/plugins/CoreTests.license
lib/ugene/plugins/CoreTests.plugin
lib/ugene/plugins/GUITestBase.license
@@ -26,12 +34,8 @@ 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
@@ -46,16 +50,14 @@ lib/ugene/plugins/enzymes.license
lib/ugene/plugins/enzymes.plugin
lib/ugene/plugins/external_tool_support.license
lib/ugene/plugins/external_tool_support.plugin
+lib/ugene/plugins/genecut.license
+lib/ugene/plugins/genecut.plugin
lib/ugene/plugins/genome_aligner.license
lib/ugene/plugins/genome_aligner.plugin
lib/ugene/plugins/gor4.license
lib/ugene/plugins/gor4.plugin
lib/ugene/plugins/hmm2.license
lib/ugene/plugins/hmm2.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/libGUITestBase.so
lib/ugene/plugins/libannotator.so
@@ -64,9 +66,7 @@ lib/ugene/plugins/libball.so
lib/ugene/plugins/libbiostruct3d_view.so
lib/ugene/plugins/libchroma_view.so
lib/ugene/plugins/libcircular_view.so
-lib/ugene/plugins/libclark_support.so
lib/ugene/plugins/libdbi_bam.so
-lib/ugene/plugins/libdiamond_support.so
lib/ugene/plugins/libdna_export.so
lib/ugene/plugins/libdna_flexibility.so
lib/ugene/plugins/libdna_graphpack.so
@@ -74,15 +74,11 @@ lib/ugene/plugins/libdna_stat.so
lib/ugene/plugins/libdotplot.so
lib/ugene/plugins/libenzymes.so
lib/ugene/plugins/libexternal_tool_support.so
+lib/ugene/plugins/libgenecut.so
lib/ugene/plugins/libgenome_aligner.so
lib/ugene/plugins/libgor4.so
lib/ugene/plugins/libhmm2.so
-lib/ugene/plugins/libkalign.so
-lib/ugene/plugins/libkraken_support.so
lib/ugene/plugins/liblinkdata_support.so
-lib/ugene/plugins/libmetaphlan2_support.so
-lib/ugene/plugins/libngs_reads_classification.so
-lib/ugene/plugins/libopencl_support.so
lib/ugene/plugins/liborf_marker.so
lib/ugene/plugins/libpcr.so
lib/ugene/plugins/libperf_monitor.so
@@ -99,16 +95,9 @@ lib/ugene/plugins/libtest_runner.so
lib/ugene/plugins/libumuscle.so
lib/ugene/plugins/libvariants.so
lib/ugene/plugins/libweight_matrix.so
-lib/ugene/plugins/libwevote_support.so
lib/ugene/plugins/libworkflow_designer.so
lib/ugene/plugins/linkdata_support.license
lib/ugene/plugins/linkdata_support.plugin
-lib/ugene/plugins/metaphlan2_support.license
-lib/ugene/plugins/metaphlan2_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
lib/ugene/plugins/orf_marker.plugin
lib/ugene/plugins/pcr.license
@@ -141,1178 +130,17 @@ 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
+@(root,wheel,755) lib/ugene/plugins_checker
lib/ugene/transl_ru.qm
lib/ugene/transl_tr.qm
-lib/ugene/ugene
-lib/ugene/ugenecl
-lib/ugene/ugenem
-lib/ugene/ugeneui
-share/man/man1/ugene.1.gz
+@(root,wheel,755) lib/ugene/ugene
+@(root,wheel,755) lib/ugene/ugenecl
+@(root,wheel,755) lib/ugene/ugenem
+@(root,wheel,755) lib/ugene/ugeneui
share/applications/ugene.desktop
-share/icons/hicolor/32x32/mimetypes/application-x-ugene-ext.png
+share/man/man1/ugene.1.gz
share/mime/packages/application-x-ugene.xml
+share/pixmaps/application-x-ugene-ext.png
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
-%%DATADIR%%/back_translation/Bacteria/Haemophilus_influenzae.cut
-%%DATADIR%%/back_translation/Bacteria/Helicobacter_pylori.cut
-%%DATADIR%%/back_translation/Bacteria/Listeria_monocytogenes.cut
-%%DATADIR%%/back_translation/Bacteria/Neisseria_meningitidis.cut
-%%DATADIR%%/back_translation/Bacteria/Salmonella_typhimurium_LT2.cut
-%%DATADIR%%/back_translation/Bacteria/Streptomyces_coelicolor_A3(2).cut
-%%DATADIR%%/back_translation/Bacteria/Sulfolobus_solfataricus_P2.cut
-%%DATADIR%%/back_translation/Invertebrates/Apis_mellifera_(honey_bee).cut
-%%DATADIR%%/back_translation/Invertebrates/Caenorhabditis_elegans.cut
-%%DATADIR%%/back_translation/Invertebrates/Drosophila_melanogaster_(fruit_fly).cut
-%%DATADIR%%/back_translation/Invertebrates/Plasmodium_falciparum_(malaria_parasite_P._falciparum).cut
-%%DATADIR%%/back_translation/Invertebrates/mitochondrion_Caenorhabditis_elegans.cut
-%%DATADIR%%/back_translation/Invertebrates/mitochondrion_Drosophila_melanogaster_(fruit_fly).cut
-%%DATADIR%%/back_translation/Mammalia/Bos_taurus_(cow).cut
-%%DATADIR%%/back_translation/Mammalia/Canis_familiaris_(dog).cut
-%%DATADIR%%/back_translation/Mammalia/Sus_scrofa_(pig).cut
-%%DATADIR%%/back_translation/Mammalia/mitochondrion_Bos_taurus_(cow).cut
-%%DATADIR%%/back_translation/Mammalia/mitochondrion_Sus_scrofa_(pig).cut
-%%DATADIR%%/back_translation/Plants/Arabidopsis_thaliana_(thale_cress).cut
-%%DATADIR%%/back_translation/Plants/Oryza_sativa.cut
-%%DATADIR%%/back_translation/Plants/Zea_mays.cut
-%%DATADIR%%/back_translation/Primates/Homo_sapiens_(human).cut
-%%DATADIR%%/back_translation/Primates/Pan_troglodytes_(chimpanzee).cut
-%%DATADIR%%/back_translation/Primates/mitochondrion_Homo_sapiens_(human).cut
-%%DATADIR%%/back_translation/Primates/mitochondrion_Pan_troglodytes_(chimpanzee).cut
-%%DATADIR%%/back_translation/Rodents/Mus_musculus_(house_mouse).cut
-%%DATADIR%%/back_translation/Rodents/Rattus_norvegicus_(Norway_rat).cut
-%%DATADIR%%/back_translation/Vertebrates/Gallus_gallus_(chicken).cut
-%%DATADIR%%/back_translation/Vertebrates/Takifugu_rubripes_(Fugu_rubripes).cut
-%%DATADIR%%/back_translation/Vertebrates/Xenopus_laevis_(African_clawed_frog).cut
-%%DATADIR%%/back_translation/Vertebrates/mitochondrion_Gallus_gallus_(chicken).cut
-%%DATADIR%%/back_translation/Vertebrates/mitochondrion_Takifugu_rubripes_(Fugu_rubripes).cut
-%%DATADIR%%/back_translation/Viruses/Human_immunodeficiency_virus_1_(HIV-1).cut
-%%DATADIR%%/back_translation/Viruses/Influenza_A_virus.cut
-%%DATADIR%%/back_translation/Yeast/Saccharomyces_cerevisiae_(baker's_yeast).cut
-%%DATADIR%%/back_translation/tables.xml
-%%DATADIR%%/biostruct3d_plugin/BioStruct3DLinks.txt
-%%DATADIR%%/cmdline/align-clustalo.uwl
-%%DATADIR%%/cmdline/align-clustalw.uwl
-%%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
-%%DATADIR%%/cmdline/extract-sequence.uwl
-%%DATADIR%%/cmdline/extract_consensus_sequence.uwl
-%%DATADIR%%/cmdline/extract_consensus_string.uwl
-%%DATADIR%%/cmdline/extract_coverage.uwl
-%%DATADIR%%/cmdline/fetch-sequence.uwl
-%%DATADIR%%/cmdline/find-orfs.uwl
-%%DATADIR%%/cmdline/find-repeats.uwl
-%%DATADIR%%/cmdline/find-sw.uwl
-%%DATADIR%%/cmdline/gene-by-gene.uwl
-%%DATADIR%%/cmdline/generate-dna.uwl
-%%DATADIR%%/cmdline/hmm2-build.uwl
-%%DATADIR%%/cmdline/hmm2-search.uwl
-%%DATADIR%%/cmdline/hmm3-build-and-search.uwl
-%%DATADIR%%/cmdline/hmm3-search.uwl
-%%DATADIR%%/cmdline/join-quality.uwl
-%%DATADIR%%/cmdline/local-blast+.uwl
-%%DATADIR%%/cmdline/pfm-build.uwl
-%%DATADIR%%/cmdline/pfm-search.uwl
-%%DATADIR%%/cmdline/pwm-build.uwl
-%%DATADIR%%/cmdline/pwm-search.uwl
-%%DATADIR%%/cmdline/query.uwl
-%%DATADIR%%/cmdline/remote-request.uwl
-%%DATADIR%%/cmdline/revcompl.uwl
-%%DATADIR%%/cmdline/sitecon-build.uwl
-%%DATADIR%%/cmdline/sitecon-search.uwl
-%%DATADIR%%/cmdline/snp.uwl
-%%DATADIR%%/custom_annotations/plasmid_features.txt
-%%DATADIR%%/enzymes/2013_08_01.bairoch.gz
-%%DATADIR%%/genome_lengths/danRer7.genome
-%%DATADIR%%/genome_lengths/ecoli.genome
-%%DATADIR%%/genome_lengths/hg18.genome
-%%DATADIR%%/genome_lengths/hg19.genome
-%%DATADIR%%/genome_lengths/mm10.genome
-%%DATADIR%%/genome_lengths/mm8.genome
-%%DATADIR%%/genome_lengths/mm9.genome
-%%DATADIR%%/genome_lengths/test.genome
-%%DATADIR%%/license
-%%DATADIR%%/position_weight_matrix/JASPAR/all_jaspar.csv
-%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0265.1.pfm
-%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0266.1.pfm
-%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0267.1.pfm
-%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0268.1.pfm
-%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0269.1.pfm
-%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0270.1.pfm
-%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0271.1.pfm
-%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0272.1.pfm
-%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0273.1.pfm
-%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0274.1.pfm
-%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0275.1.pfm
-%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0276.1.pfm
-%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0277.1.pfm
-%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0278.1.pfm
-%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0279.1.pfm
-%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0280.1.pfm
-%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0281.1.pfm
-%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0282.1.pfm
-%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0283.1.pfm
-%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0284.1.pfm
-%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0285.1.pfm
-%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0286.1.pfm
-%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0287.1.pfm
-%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0288.1.pfm
-%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0289.1.pfm
-%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0290.1.pfm
-%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0291.1.pfm
-%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0292.1.pfm
-%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0293.1.pfm
-%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0294.1.pfm
-%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0295.1.pfm
-%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0296.1.pfm
-%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0297.1.pfm
-%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0298.1.pfm
-%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0299.1.pfm
-%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0300.1.pfm
-%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0301.1.pfm
-%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0302.1.pfm
-%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0303.1.pfm
-%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0304.1.pfm
-%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0305.1.pfm
-%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0306.1.pfm
-%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0307.1.pfm
-%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0308.1.pfm
-%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0309.1.pfm
-%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0310.1.pfm
-%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0311.1.pfm
-%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0312.1.pfm
-%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0313.1.pfm
-%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0314.1.pfm
-%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0315.1.pfm
-%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0316.1.pfm
-%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0317.1.pfm
-%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0318.1.pfm
-%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0319.1.pfm
-%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0320.1.pfm
-%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0321.1.pfm
-%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0322.1.pfm
-%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0323.1.pfm
-%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0324.1.pfm
-%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0325.1.pfm
-%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0326.1.pfm
-%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0327.1.pfm
-%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0328.1.pfm
-%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0329.1.pfm
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