diff --git a/MOVED b/MOVED index 30ff7633f806..57e08175d120 100644 --- a/MOVED +++ b/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 diff --git a/biology/Makefile b/biology/Makefile index 12be99b39569..6cc61e425576 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -162,6 +162,7 @@ SUBDIR += treepuzzle SUBDIR += trimadap SUBDIR += trimmomatic + SUBDIR += ugene SUBDIR += vcflib SUBDIR += vcftools SUBDIR += velvet diff --git a/biology/ugene/Makefile b/biology/ugene/Makefile new file mode 100644 index 000000000000..7a8130374aed --- /dev/null +++ b/biology/ugene/Makefile @@ -0,0 +1,65 @@ +# Created by: Hannes Hauswedell +# $FreeBSD$ + +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 + +.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 diff --git a/biology/ugene/distinfo b/biology/ugene/distinfo new file mode 100644 index 000000000000..5e12e8d62fc0 --- /dev/null +++ b/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 diff --git a/biology/ugene/files/patch-src_corelibs_U2Private_U2Private.pro b/biology/ugene/files/patch-src_corelibs_U2Private_U2Private.pro new file mode 100644 index 000000000000..73f2d4038887 --- /dev/null +++ b/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 { 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 new file mode 100644 index 000000000000..cc2164cb1db0 --- /dev/null +++ b/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 + #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" + 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 new file mode 100644 index 000000000000..8dfdd9b7d53f --- /dev/null +++ b/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 + +-#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); diff --git a/biology/ugene/files/patch-src_plugins__checker_src_Main.cpp b/biology/ugene/files/patch-src_plugins__checker_src_Main.cpp new file mode 100644 index 000000000000..bd0d64942c01 --- /dev/null +++ b/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 + #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){ +@@ -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 new file mode 100644 index 000000000000..917fc096b4c4 --- /dev/null +++ b/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 + #include + #include +-#include ++//#include + + // 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; + } diff --git a/biology/ugene/files/patch-src_ugeneui_src_Main.cpp b/biology/ugene/files/patch-src_ugeneui_src_Main.cpp new file mode 100644 index 000000000000..e5dcadcdea21 --- /dev/null +++ b/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 + #include + #include +-#include ++//#include + + #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; + } diff --git a/biology/ugene/files/patch-ugene.pro b/biology/ugene/files/patch-ugene.pro new file mode 100644 index 000000000000..8962a9edc02e --- /dev/null +++ b/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 ) { diff --git a/biology/ugene/pkg-descr b/biology/ugene/pkg-descr new file mode 100644 index 000000000000..a5e84919dfc2 --- /dev/null +++ b/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/ diff --git a/biology/ugene/pkg-plist b/biology/ugene/pkg-plist new file mode 100644 index 000000000000..bf723b18b5e0 --- /dev/null +++ b/biology/ugene/pkg-plist @@ -0,0 +1,1478 @@ +bin/ugene +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/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/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/annotator.license +lib/ugene/plugins/annotator.plugin +lib/ugene/plugins/api_tests.license +lib/ugene/plugins/api_tests.plugin +lib/ugene/plugins/ball.license +lib/ugene/plugins/ball.plugin +lib/ugene/plugins/biostruct3d_view.license +lib/ugene/plugins/biostruct3d_view.plugin +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 +lib/ugene/plugins/dna_flexibility.plugin +lib/ugene/plugins/dna_graphpack.license +lib/ugene/plugins/dna_graphpack.plugin +lib/ugene/plugins/dna_stat.license +lib/ugene/plugins/dna_stat.plugin +lib/ugene/plugins/dotplot.license +lib/ugene/plugins/dotplot.plugin +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/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/libCoreTests.so.1 +lib/ugene/plugins/libCoreTests.so.1.0 +lib/ugene/plugins/libCoreTests.so.1.0.0 +lib/ugene/plugins/libannotator.so +lib/ugene/plugins/libannotator.so.1 +lib/ugene/plugins/libannotator.so.1.0 +lib/ugene/plugins/libannotator.so.1.0.0 +lib/ugene/plugins/libapi_tests.so +lib/ugene/plugins/libapi_tests.so.1 +lib/ugene/plugins/libapi_tests.so.1.0 +lib/ugene/plugins/libapi_tests.so.1.0.0 +lib/ugene/plugins/libball.so +lib/ugene/plugins/libball.so.1 +lib/ugene/plugins/libball.so.1.0 +lib/ugene/plugins/libball.so.1.0.0 +lib/ugene/plugins/libbiostruct3d_view.so +lib/ugene/plugins/libbiostruct3d_view.so.1 +lib/ugene/plugins/libbiostruct3d_view.so.1.0 +lib/ugene/plugins/libbiostruct3d_view.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 +lib/ugene/plugins/libdna_export.so +lib/ugene/plugins/libdna_export.so.1 +lib/ugene/plugins/libdna_export.so.1.0 +lib/ugene/plugins/libdna_export.so.1.0.0 +lib/ugene/plugins/libdna_flexibility.so +lib/ugene/plugins/libdna_flexibility.so.1 +lib/ugene/plugins/libdna_flexibility.so.1.0 +lib/ugene/plugins/libdna_flexibility.so.1.0.0 +lib/ugene/plugins/libdna_graphpack.so +lib/ugene/plugins/libdna_graphpack.so.1 +lib/ugene/plugins/libdna_graphpack.so.1.0 +lib/ugene/plugins/libdna_graphpack.so.1.0.0 +lib/ugene/plugins/libdna_stat.so +lib/ugene/plugins/libdna_stat.so.1 +lib/ugene/plugins/libdna_stat.so.1.0 +lib/ugene/plugins/libdna_stat.so.1.0.0 +lib/ugene/plugins/libdotplot.so +lib/ugene/plugins/libdotplot.so.1 +lib/ugene/plugins/libdotplot.so.1.0 +lib/ugene/plugins/libdotplot.so.1.0.0 +lib/ugene/plugins/libenzymes.so +lib/ugene/plugins/libenzymes.so.1 +lib/ugene/plugins/libenzymes.so.1.0 +lib/ugene/plugins/libenzymes.so.1.0.0 +lib/ugene/plugins/libexternal_tool_support.so 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