- Resurrect and unbreak by updating to version 34.0

- Stop providing outdated offline PDF documentation,
  users are advised to use the online files instead

MOVED

@@ -14565,7 +14565,6 @@ biology/consed||2020-05-05|Has expired: Broken for more than 6 months
 biology/plinkseq||2020-05-05|Has expired: Broken for more than 6 months
 biology/seqtools||2020-05-05|Has expired: Broken for more than 6 months
 biology/t_coffee||2020-05-05|Has expired: Broken for more than 6 months
-biology/ugene||2020-05-05|Has expired: Broken for more than 6 months
 comms/ath3k-firmware||2020-05-05|Has expired: Broken for more than 6 months
 comms/geoid||2020-05-05|Has expired: Broken for more than 6 months
 comms/jerm||2020-05-05|Has expired: Broken for more than 6 months

biology/Makefile

@@ -162,6 +162,7 @@
     SUBDIR += treepuzzle
     SUBDIR += trimadap
     SUBDIR += trimmomatic
+    SUBDIR += ugene
     SUBDIR += vcflib
     SUBDIR += vcftools
     SUBDIR += velvet

biology/ugene/Makefile

@@ -0,0 +1,65 @@
+# Created by: Hannes Hauswedell <h2+fbsdports@fsfe.org>
+# $FreeBSD$
+
+PORTNAME=	ugene
+PORTVERSION=	34.0
+CATEGORIES=	biology science
+
+MAINTAINER=	h2+fbsdports@fsfe.org
+COMMENT=	Free, open-source, cross-platform bioinformatics toolkit
+
+LICENSE=	GPLv2+
+LICENSE_FILE=	${WRKSRC}/LICENSE.txt
+
+RUN_DEPENDS=	bash:shells/bash
+
+BROKEN_aarch64=	Fails to build: invokes x86 asm
+
+USE_GITHUB=	yes
+GH_ACCOUNT=	ugeneunipro
+
+USES=		desktop-file-utils gl qmake qt:5 shared-mime-info xorg
+USE_GL=		gl glu
+USE_QT=		buildtools_build linguisttools_build \
+		core declarative gui opengl location network printsupport \
+		script scripttools sql svg testlib webchannel webengine \
+		websockets widgets xml \
+		imageformats_run
+USE_XORG=	x11 xtst
+
+QMAKE_ARGS=	INSTALL_PREFIX="${PREFIX}" UGENE_INSTALL_DATA="${DATADIR}" \
+		INSTALL_MANDIR="${MAN1PREFIX}/man" LRELEASE="${LRELEASE}" \
+		LUPDATE="${LUPDATE}"
+ALL_TARGET=	release
+
+OPTIONS_DEFINE=	OPENCL
+
+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
+.endif
+
+.if ${MACHINE_CPU:Msse2}
+QMAKE_ARGS+=	UGENE_SSE2_DETECTED=1
+.endif
+
+post-patch:
+# yes, bash is required, stuff will not execute with sh
+	@${REINPLACE_CMD} -e 's|/bin/bash|/usr/bin/env bash|' \
+		${WRKSRC}/src/gen_bin_script.cmd \
+		${WRKSRC}/installer/_common_data/ugene
+	@${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 '422s|NULL|0|' \
+		${WRKSRC}/src/plugins/smith_waterman/src/SmithWatermanAlgorithmOPENCL.cpp
+
+.include <bsd.port.post.mk>

biology/ugene/distinfo

@@ -0,0 +1,3 @@
+TIMESTAMP = 1584963065
+SHA256 (ugeneunipro-ugene-34.0_GH0.tar.gz) = 569b9997497680412e03d821c7d48903830012a65c5899a5aea3cb80e9f4ee25
+SIZE (ugeneunipro-ugene-34.0_GH0.tar.gz) = 23406266

biology/ugene/files/patch-src_corelibs_U2Private_U2Private.pro

@@ -0,0 +1,41 @@
+--- 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 {

biology/ugene/files/patch-src_libs__3rdparty_QSpec_src_drivers_GTKeyboardDriverLinux.cpp

@@ -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"
+ 

biology/ugene/files/patch-src_libs__3rdparty_QSpec_src_drivers_GTMouseDriverLinux.cpp

@@ -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);

biology/ugene/files/patch-src_plugins__checker_src_Main.cpp

@@ -0,0 +1,31 @@
+--- 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() {
+ 
+ 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){
+@@ -141,7 +143,7 @@ int main(int argc, char **argv)
+     delete cmdLineRegistry;
+     appContext->setCMDLineRegistry(NULL);
+ 
+-    CrashHandler::shutdown();
++    //CrashHandler::shutdown();
+ 
+     return rc;
+ }

biology/ugene/files/patch-src_ugenecl_src_Main.cpp

@@ -0,0 +1,36 @@
+--- src/ugenecl/src/Main.cpp.orig	2018-08-16 13:59:20 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();
+     }
+@@ -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){
+@@ -617,7 +619,7 @@ int main(int argc, char **argv)
+     delete pwr;
+     appContext->setAlignmentAlgorithmsRegistry(NULL);
+ 
+-    CrashHandler::shutdown();
++    //CrashHandler::shutdown();
+ 
+     return rc;
+ }

biology/ugene/files/patch-src_ugeneui_src_Main.cpp

@@ -0,0 +1,36 @@
+--- src/ugeneui/src/Main.cpp.orig	2018-08-16 13:59:19 UTC
++++ src/ugeneui/src/Main.cpp
+@@ -136,7 +136,7 @@
+ #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"
+@@ -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 );
+ 
+@@ -973,7 +975,7 @@ int main(int argc, char **argv)
+     }
+ 
+     UgeneUpdater::onClose();
+-    CrashHandler::shutdown();
++    //CrashHandler::shutdown();
+ 
+     return rc;
+ }

biology/ugene/files/patch-ugene.pro

@@ -0,0 +1,29 @@
+--- 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 \
+@@ -141,16 +140,8 @@ UGENE_TRANSL_QM_TARGET_DIR = $$OUT_PWD/src/_debug $$OU
+ win32 : UGENE_DEV_NULL = nul
+ unix : UGENE_DEV_NULL = /dev/null
+ 
+-UGENE_LRELEASE =
+-UGENE_LUPDATE =
+-message(Using QT from $$[QT_INSTALL_BINS])
+-system($$[QT_INSTALL_BINS]/lrelease-qt5 -version > $$UGENE_DEV_NULL 2> $$UGENE_DEV_NULL) {
+-    UGENE_LRELEASE = $$[QT_INSTALL_BINS]/lrelease-qt5
+-    UGENE_LUPDATE = $$[QT_INSTALL_BINS]/lupdate-qt5
+-} else : system($$[QT_INSTALL_BINS]/lrelease -version > $$UGENE_DEV_NULL 2> $$UGENE_DEV_NULL) {
+-    UGENE_LRELEASE = $$[QT_INSTALL_BINS]/lrelease
+-    UGENE_LUPDATE = $$[QT_INSTALL_BINS]/lupdate
+-}
++UGENE_LRELEASE = $$LRELEASE
++UGENE_LUPDATE = $$LUPDATE
+ 
+ #foreach 'language'
+ for( i, UGENE_TRANSL_IDX ) {

biology/ugene/pkg-descr

@@ -0,0 +1,12 @@
+Unipro UGENE is multiplatform, open-source software with the main goal of
+assisting molecular biologists without much expertise in bioinformatics to
+manage, analyze, and visualize their data.  UGENE integrates widely used
+bioinformatics tools within one common user interface.
+
+UGENE toolkit supports multiple biological data formats and allows the
+retrieval of data from remote data sources.  It provides visualization
+modules for biological objects such as annotated genome sequences, Next
+Generation Sequencing (NGS) assembly data, multiple sequence alignments,
+phylogenetic trees, and 3D structures.
+
+WWW: http://ugene.unipro.ru/