Date: Thu, 16 Jan 2014 17:17:16 +0000 (UTC) From: Alexey Dokuchaev <danfe@FreeBSD.org> To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r339938 - in head/biology/ugene: . files Message-ID: <201401161717.s0GHHGZk004570@svn.freebsd.org>
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Author: danfe Date: Thu Jan 16 17:17:15 2014 New Revision: 339938 URL: http://svnweb.freebsd.org/changeset/ports/339938 QAT: https://qat.redports.org/buildarchive/r339938/ Log: - Update to version 1.13.0 and improve FreeBSD support; it also builds pretty cleanly with GCC v4.2, v4.6, and Clang (modulo a few warnings) - Sadly, do not use PORTDOCS: since DOCSDIR is set to be inside DATADIR, and will get appended to PLIST after @dirrm %%DATADIR%%, which upsets sanity checking tools; instead, list the docs explicitly in DISTFILES and add them to pkg-plist (guarded by %%PORTDOCS%%) Tested on: i386 (only) Added: head/biology/ugene/files/patch-src-corelibs-U2Core-src-globals-AppResources.cpp (contents, props changed) head/biology/ugene/files/patch-src-shtirlitz-Shtirlitz.cpp (contents, props changed) head/biology/ugene/files/patch-src-ugenem-src-SendReportDialog.cpp (contents, props changed) head/biology/ugene/files/patch-src-ugeneui-src-Main.cpp (contents, props changed) Deleted: head/biology/ugene/files/patch-clang-fixes head/biology/ugene/files/patch-gtest-std::tr1::tuple-fix Modified: head/biology/ugene/Makefile head/biology/ugene/distinfo head/biology/ugene/pkg-plist Modified: head/biology/ugene/Makefile ============================================================================== --- head/biology/ugene/Makefile Thu Jan 16 17:16:10 2014 (r339937) +++ head/biology/ugene/Makefile Thu Jan 16 17:17:15 2014 (r339938) @@ -2,10 +2,11 @@ # $FreeBSD$ PORTNAME= ugene -DISTVERSION= 1.12.3 +DISTVERSION= 1.13.0 CATEGORIES= biology MASTER_SITES= http://ugene.unipro.ru/downloads/ -DISTFILES= ${DISTNAME}${EXTRACT_SUFX} ${PORTDOCS} +DISTFILES= ${DISTNAME}${EXTRACT_SUFX} QueryDesigner_UserManual.pdf \ + UniproUGENE_UserManual.pdf WorkflowDesigner_UserManual.pdf DIST_SUBDIR= ${PORTNAME} EXTRACT_ONLY= ${DISTNAME}${EXTRACT_SUFX} @@ -22,7 +23,8 @@ RUN_DEPENDS= bash:${PORTSDIR}/shells/bas USES= qmake USE_GL= glu USE_QT4= gui webkit xml svg linguist_build moc_build qmake_build \ - qtestlib_build rcc_build uic_build imageformats_run + qtestlib_build rcc_build uic_build imageformats_run \ + scripttools_build USE_XORG= xtst USE_LDCONFIG= yes INSTALLS_ICONS= yes @@ -32,14 +34,13 @@ QMAKE_ARGS= INSTALL_PREFIX=${PREFIX} UGE ALL_TARGET= release DOCSDIR= ${DATADIR}/manuals -PORTDOCS= QueryDesigner_UserManual.pdf UniproUGENE_UserManual.pdf \ - WorkflowDesigner_UserManual.pdf OPTIONS_DEFINE= DOCS DOCS_DESC= Install official UGENE documentation (PDF) .include <bsd.port.pre.mk> +# Required for Google Test code .if ${OSVERSION} > 1000054 CXXFLAGS+= -std=c++11 .endif @@ -64,10 +65,36 @@ post-patch: @${REINPLACE_CMD} -e 's|/bin/bash|/usr/bin/env bash|' \ ${WRKSRC}/src/gen_bin_script.cmd \ ${WRKSRC}/installer/_common_data/ugene -# remove BOM from files and non-latin comments; gcc 4.2 does not like them - @${REINPLACE_CMD} -e '1s|^[^/]*|| ; /lose sequence view,/d' \ - ${WRKSRC}/src/plugins/GUITestBase/src/tests/common_scenarios/smith_waterman_dialog/GTTestsSWDialog.cpp \ - ${WRKSRC}/src/plugins/GUITestBase/src/tests/common_scenarios/repeat_finder/GTTestsRepeatFinder.cpp + @${REINPLACE_CMD} -e '30s|^|#include <time.h>|' \ + ${WRKSRC}/src/plugins/dbi_bam/src/BAMDbiPlugin.h + @${REINPLACE_CMD} -e 's|runTime=NULL|runTime=0|' \ + ${WRKSRC}/src/plugins/test_runner/src/TestViewReporter.h + @${REINPLACE_CMD} -e 's|Q_OS_LINUX|Q_OS_UNIX|' \ + ${WRKSRC}/src/ugenem/src/main.cpp + @(cd ${WRKSRC}/src/plugins/external_tool_support/src && \ + ${REINPLACE_CMD} -e 's/LINUX) || defined(Q_OS_MAC/UNIX/' \ + ExternalToolSupportPlugin.cpp \ + R/RSupport.cpp \ + blast/BlastAllSupport.cpp \ + blast/FormatDBSupport.cpp \ + blast_plus/BlastDBCmdSupport.cpp \ + blast_plus/BlastPlusSupport.cpp \ + bowtie/BowtieSupport.cpp \ + bowtie2/Bowtie2Support.cpp \ + bwa/BwaSupport.cpp \ + cap3/CAP3Support.cpp \ + clustalo/ClustalOSupport.cpp \ + clustalw/ClustalWSupport.cpp \ + cufflinks/CufflinksSupport.cpp \ + mrbayes/MrBayesSupport.cpp \ + perl/PerlSupport.cpp \ + python/PythonSupport.cpp \ + samtools/BcfToolsSupport.cpp \ + samtools/SamToolsExtToolSupport.cpp \ + spidey/SpideySupport.cpp \ + tcoffee/TCoffeeSupport.cpp \ + tophat/TopHatSupport.cpp \ + utils/ExternalToolSearchTask.cpp) post-configure: @${REINPLACE_CMD} -e '/^LFLAGS/s,-pthread,-lexecinfo &,' \ Modified: head/biology/ugene/distinfo ============================================================================== --- head/biology/ugene/distinfo Thu Jan 16 17:16:10 2014 (r339937) +++ head/biology/ugene/distinfo Thu Jan 16 17:17:15 2014 (r339938) @@ -1,5 +1,5 @@ -SHA256 (ugene/ugene-1.12.3.tar.gz) = 6642ec6ef5110b50b38c9620be4a98101d9a7b325a61a202ee7e0f2c67d45496 -SIZE (ugene/ugene-1.12.3.tar.gz) = 17611949 +SHA256 (ugene/ugene-1.13.0.tar.gz) = 65bd8c343bb18a2aece4b0b9f703435727f1523b5a7344f43fe5e176b9428a3f +SIZE (ugene/ugene-1.13.0.tar.gz) = 19079436 SHA256 (ugene/QueryDesigner_UserManual.pdf) = 3c5bd735c02b7ac24bd319823fde2d175b750adc1c37fe7b17e2009452a00ddd SIZE (ugene/QueryDesigner_UserManual.pdf) = 1306825 SHA256 (ugene/UniproUGENE_UserManual.pdf) = 6c682c86f47a4c337eb4acdf0ae23ffa1b7fef1337d11e631655bfc943167b46 Added: head/biology/ugene/files/patch-src-corelibs-U2Core-src-globals-AppResources.cpp ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/ugene/files/patch-src-corelibs-U2Core-src-globals-AppResources.cpp Thu Jan 16 17:17:15 2014 (r339938) @@ -0,0 +1,73 @@ +--- src/corelibs/U2Core/src/globals/AppResources.cpp.orig ++++ src/corelibs/U2Core/src/globals/AppResources.cpp +@@ -35,6 +35,10 @@ + #include <proc/readproc.h> + #endif + ++#if defined(Q_OS_LINUX) || defined(Q_OS_FREEBSD) ++#include <unistd.h> // for sysconf(3) and getpid(2) ++#endif ++ + #ifdef Q_OS_WIN + #include <windows.h> + #include <Psapi.h> +@@ -88,17 +92,15 @@ int AppResourcePool::getTotalPhysicalMem + coreLog.error("Total physical memory: getting info error"); + } + +-#elif defined(Q_OS_LINUX) +- QProcess p; +- p.start("awk", QStringList() << "/MemTotal/ {print $2}" << "/proc/meminfo"); +- p.waitForFinished(); +- QString memory = p.readAllStandardOutput(); +- p.close(); +- bool ok = false; +- qlonglong output_mem = memory.toLongLong(&ok); +- if (ok) { +- totalPhysicalMemory = output_mem / 1024; +- } ++#elif defined(Q_OS_LINUX) || defined(Q_OS_FREEBSD) ++ long pagesize = sysconf(_SC_PAGESIZE); ++ long numpages = sysconf(_SC_PHYS_PAGES); ++ ++ // Assume that page size is always a multiple of 1024, so it can be ++ // divided without losing any precision. On the other hand, number ++ // of pages would hardly overflow `long' when multiplied by a small ++ // number (number of pages / 1024), so we should be safe here. ++ totalPhysicalMemory = (int)(numpages * (pagesize / 1024) / 1024); + + #elif defined(Q_OS_MAC) + // TODO +@@ -143,15 +145,27 @@ void AppResourcePool::setMaxMemorySizeIn + + size_t AppResourcePool::getCurrentAppMemory() { + +-#ifdef Q_OS_LINUX +- struct proc_t usage; +- //look_up_our_self(&usage); +- return usage.vsize; +-#endif + #ifdef Q_OS_WIN32 + PROCESS_MEMORY_COUNTERS memCounter; + bool result = GetProcessMemoryInfo(GetCurrentProcess(), &memCounter, sizeof( memCounter )); + return memCounter.WorkingSetSize; ++#elif defined(Q_OS_LINUX) ++ struct proc_t usage; ++ //look_up_our_self(&usage); ++ return usage.vsize; ++#elif defined(Q_OS_FREEBSD) ++ QProcess p; ++ p.start("ps", QStringList() << "-o" << "vsize=" << "-p" << QString("%1").arg(getpid())); ++ p.waitForFinished(); ++ QString ps_vsize = p.readAllStandardOutput(); ++ p.close(); ++ bool ok = false; ++ qlonglong output_mem = ps_vsize.toLongLong(&ok); ++ if (ok) { ++ return output_mem / 1024; ++ } ++#else ++ coreLog.error("Current application memory: Unsupported OS"); + #endif + } + Added: head/biology/ugene/files/patch-src-shtirlitz-Shtirlitz.cpp ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/ugene/files/patch-src-shtirlitz-Shtirlitz.cpp Thu Jan 16 17:17:15 2014 (r339938) @@ -0,0 +1,14 @@ +--- src/ugeneui/src/shtirlitz/Shtirlitz.cpp.orig ++++ src/ugeneui/src/shtirlitz/Shtirlitz.cpp +@@ -239,7 +239,10 @@ void Shtirlitz::getOsNameAndVersion( QSt + version = QString::number(QSysInfo::MacintoshVersion); + #elif defined(Q_OS_LINUX) + name = "Linux"; +- Q_UNUSED(version);//no version is available :( ++ Q_UNUSED(version); //no version is available :( ++#elif defined(Q_OS_FREEBSD) ++ name = "FreeBSD"; ++ Q_UNUSED(version); //no version is available :( + #else + name = "Other"; + #endif Added: head/biology/ugene/files/patch-src-ugenem-src-SendReportDialog.cpp ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/ugene/files/patch-src-ugenem-src-SendReportDialog.cpp Thu Jan 16 17:17:15 2014 (r339938) @@ -0,0 +1,49 @@ +--- src/ugenem/src/SendReportDialog.cpp.orig ++++ src/ugenem/src/SendReportDialog.cpp +@@ -44,6 +44,10 @@ + #include <Winbase.h> //for IsProcessorFeaturePresent + #endif + ++#if defined(Q_OS_LINUX) || defined(Q_OS_FREEBSD) ++#include <unistd.h> // for sysconf(3) ++#endif ++ + #define HOST_URL "http://ugene.unipro.ru" + //#define HOST_URL "http://127.0.0.1" + #define DESTINATION_URL_KEEPER_PAGE "/crash_reports_dest.html" +@@ -241,6 +245,8 @@ QString ReportSender::getOSVersion() { + + #elif defined(Q_OS_LINUX) + result = "Linux"; ++#elif defined(Q_OS_FREEBSD) ++ result = "FreeBSD"; + #elif defined(Q_OS_MAC) + result = "Mac "; + switch (QSysInfo::MacintoshVersion){ +@@ -304,17 +310,15 @@ int ReportSender::getTotalPhysicalMemory + totalPhysicalMemory = memory_status.ullTotalPhys / (1024 * 1024); + } + +-#elif defined(Q_OS_LINUX) +- QProcess p; +- p.start("awk", QStringList() << "/MemTotal/ {print $2}" << "/proc/meminfo"); +- p.waitForFinished(); +- QString memory = p.readAllStandardOutput(); +- p.close(); +- bool ok = false; +- qlonglong output_mem = memory.toLongLong(&ok); +- if (ok) { +- totalPhysicalMemory = output_mem / 1024; +- } ++#elif defined(Q_OS_LINUX) || defined(Q_OS_FREEBSD) ++ long pagesize = sysconf(_SC_PAGESIZE); ++ long numpages = sysconf(_SC_PHYS_PAGES); ++ ++ // Assume that page size is always a multiple of 1024, so it can be ++ // divided without losing any precision. On the other hand, number ++ // of pages would hardly overflow `long' when multiplied by a small ++ // number (number of pages / 1024), so we should be safe here. ++ totalPhysicalMemory = (int)(numpages * (pagesize / 1024) / 1024); + + #elif defined(Q_OS_MAC) + // TODO Added: head/biology/ugene/files/patch-src-ugeneui-src-Main.cpp ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/ugene/files/patch-src-ugeneui-src-Main.cpp Thu Jan 16 17:17:15 2014 (r339938) @@ -0,0 +1,20 @@ +--- src/ugeneui/src/Main.cpp.orig ++++ src/ugeneui/src/Main.cpp +@@ -164,7 +164,7 @@ static void setDataSearchPaths() { + dataSearchPaths.push_back( appDirPath+RELATIVE_DEV_DATA_DIR ); + } + +-#if (defined(Q_OS_LINUX) || defined(Q_OS_UNIX)) && defined( UGENE_DATA_DIR ) ++#if defined(Q_OS_UNIX) && defined(UGENE_DATA_DIR) + //using directory which is set during installation process on Linux + QString ugene_data_dir( UGENE_DATA_DIR ); + if( QDir(ugene_data_dir).exists() ) { +@@ -361,7 +361,7 @@ int main(int argc, char **argv) + qt_use_native_dialogs = useNative; //using local here for debugger + #endif + +-#if defined(Q_OS_MAC) || defined(Q_OS_LINUX) ++#if defined(Q_OS_UNIX) + if (envList.indexOf("UGENE_GUI_TEST=1") >= 0) { + QApplication::setAttribute(Qt::AA_DontUseNativeMenuBar); + } Modified: head/biology/ugene/pkg-plist ============================================================================== --- head/biology/ugene/pkg-plist Thu Jan 16 17:16:10 2014 (r339937) +++ head/biology/ugene/pkg-plist Thu Jan 16 17:17:15 2014 (r339938) @@ -1,14 +1,48 @@ 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/libU2Remote.so +lib/ugene/libU2Remote.so.1 +lib/ugene/libU2Remote.so.1.0 +lib/ugene/libU2Remote.so.1.0.0 +lib/ugene/libU2Script.so +lib/ugene/libU2Script.so.1 +lib/ugene/libU2Script.so.1.0 +lib/ugene/libU2Script.so.1.0.0 lib/ugene/libU2Test.so +lib/ugene/libU2Test.so.1 +lib/ugene/libU2Test.so.1.0 +lib/ugene/libU2Test.so.1.0.0 lib/ugene/libU2View.so +lib/ugene/libU2View.so.1 +lib/ugene/libU2View.so.1.0 +lib/ugene/libU2View.so.1.0.0 lib/ugene/libgtest.so lib/ugene/libgtest.so.1 lib/ugene/libgtest.so.1.0 @@ -18,8 +52,17 @@ lib/ugene/libugenedb.so.1 lib/ugene/libugenedb.so.1.0 lib/ugene/libugenedb.so.1.0.0 lib/ugene/plugins/libbrowser_support.so +lib/ugene/plugins/libbrowser_support.so.1 +lib/ugene/plugins/libbrowser_support.so.1.0 +lib/ugene/plugins/libbrowser_support.so.1.0.0 lib/ugene/plugins/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/libvariants.so +lib/ugene/plugins/libvariants.so.1 +lib/ugene/plugins/libvariants.so.1.0 +lib/ugene/plugins/libvariants.so.1.0.0 lib/ugene/plugins/linkdata_support.license lib/ugene/plugins/linkdata_support.plugin lib/ugene/plugins/variants.license @@ -69,43 +112,161 @@ lib/ugene/plugins/hmm2.plugin lib/ugene/plugins/kalign.license lib/ugene/plugins/kalign.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 +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/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/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 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+lib/ugene/plugins/libpsipred.so.1 +lib/ugene/plugins/libpsipred.so.1.0 +lib/ugene/plugins/libpsipred.so.1.0.0 lib/ugene/plugins/libptools.so +lib/ugene/plugins/libptools.so.1 +lib/ugene/plugins/libptools.so.1.0 +lib/ugene/plugins/libptools.so.1.0.0 lib/ugene/plugins/libquery_designer.so +lib/ugene/plugins/libquery_designer.so.1 +lib/ugene/plugins/libquery_designer.so.1.0 +lib/ugene/plugins/libquery_designer.so.1.0.0 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 +lib/ugene/plugins/librepeat_finder.so.1.0.0 lib/ugene/plugins/libsitecon.so +lib/ugene/plugins/libsitecon.so.1 +lib/ugene/plugins/libsitecon.so.1.0 +lib/ugene/plugins/libsitecon.so.1.0.0 lib/ugene/plugins/libsmith_waterman.so +lib/ugene/plugins/libsmith_waterman.so.1 +lib/ugene/plugins/libsmith_waterman.so.1.0 +lib/ugene/plugins/libsmith_waterman.so.1.0.0 +lib/ugene/plugins/libsnp_effect.so +lib/ugene/plugins/libsnp_effect.so.1 +lib/ugene/plugins/libsnp_effect.so.1.0 +lib/ugene/plugins/libsnp_effect.so.1.0.0 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/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/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/opencl_support.license lib/ugene/plugins/opencl_support.plugin lib/ugene/plugins/orf_marker.license @@ -132,6 +293,8 @@ lib/ugene/plugins/sitecon.license lib/ugene/plugins/sitecon.plugin lib/ugene/plugins/smith_waterman.license lib/ugene/plugins/smith_waterman.plugin +lib/ugene/plugins/snp_effect.license +lib/ugene/plugins/snp_effect.plugin lib/ugene/plugins/test_runner.license lib/ugene/plugins/test_runner.plugin %%NOX64%%lib/ugene/plugins/umuscle.license @@ -201,6 +364,7 @@ share/pixmaps/ugene.xpm %%DATADIR%%/cmdline/align.uwl %%DATADIR%%/cmdline/convert-msa.uwl %%DATADIR%%/cmdline/convert-seq.uwl +%%DATADIR%%/cmdline/das_annotation.uwl %%DATADIR%%/cmdline/extract-sequence.uwl %%DATADIR%%/cmdline/fetch-sequence.uwl %%DATADIR%%/cmdline/find-orfs.uwl @@ -222,8 +386,12 @@ share/pixmaps/ugene.xpm %%DATADIR%%/cmdline/revcompl.uwl %%DATADIR%%/cmdline/sitecon-build.uwl %%DATADIR%%/cmdline/sitecon-search.uwl +%%DATADIR%%/cmdline/snp.uwl %%DATADIR%%/enzymes/2013_08_01.bairoch.gz %%DATADIR%%/license +%%PORTDOCS%%%%DOCSDIR%%/QueryDesigner_UserManual.pdf +%%PORTDOCS%%%%DOCSDIR%%/UniproUGENE_UserManual.pdf +%%PORTDOCS%%%%DOCSDIR%%/WorkflowDesigner_UserManual.pdf %%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 @@ -973,6 +1141,8 @@ share/pixmaps/ugene.xpm %%DATADIR%%/query_samples/RepeatsWithORF.uql %%DATADIR%%/query_samples/SimpleGene.uql %%DATADIR%%/samples/ABIF/A01.abi +%%DATADIR%%/samples/ACE/K26.ace +%%DATADIR%%/samples/ACE/BL060C3.ace %%DATADIR%%/samples/Assembly/chrM.fa %%DATADIR%%/samples/Assembly/chrM.sam %%DATADIR%%/samples/Assembly/chrM.sorted.bam @@ -1105,6 +1275,13 @@ share/pixmaps/ugene.xpm %%DATADIR%%/sitecon_models/prokaryotic/TyrR.sitecon.gz %%DATADIR%%/sitecon_models/prokaryotic/fis_new1.sitecon.gz %%DATADIR%%/sitecon_models/prokaryotic/soxS.sitecon.gz +%%DATADIR%%/snp_scripts/SNPChIPTools.py +%%DATADIR%%/snp_scripts/pdb_uniprot_chain_map.lst.2 +%%DATADIR%%/snp_scripts/protstability1d.py +%%DATADIR%%/snp_scripts/protstability3d.py +%%DATADIR%%/snp_scripts/rsnp.py +%%DATADIR%%/snp_scripts/snp2pdbsite.py +%%DATADIR%%/snp_scripts/update_d_db.py %%DATADIR%%/translations.txt %%DATADIR%%/weight_matrix/blosum100.txt %%DATADIR%%/weight_matrix/blosum30.txt @@ -1195,7 +1372,6 @@ share/pixmaps/ugene.xpm %%DATADIR%%/workflow_samples/Conversions/msa2clustal.uwl %%DATADIR%%/workflow_samples/Conversions/query2alignment.uwl %%DATADIR%%/workflow_samples/Conversions/seq2gen.uwl -%%DATADIR%%/workflow_samples/Custom elements/script-create-alignment.uwl %%DATADIR%%/workflow_samples/Custom elements/script-dump-sequence-info.uwl %%DATADIR%%/workflow_samples/Custom elements/script-linkdata-fetch-seq.uwl %%DATADIR%%/workflow_samples/Custom elements/script-quality-filter.uwl @@ -1210,10 +1386,12 @@ share/pixmaps/ugene.xpm %%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_transcript_seq.uwl %%DATADIR%%/workflow_samples/NGS/tuxedo/tuxedo_main.uwl %%DATADIR%%/workflow_samples/NGS/tuxedo/tuxedo_main_paired.uwl -%%DATADIR%%/workflow_samples/NGS/tuxedo/tuxedo_multiple_dataset.uwl -%%DATADIR%%/workflow_samples/NGS/tuxedo/tuxedo_multiple_dataset_paired.uwl +%%DATADIR%%/workflow_samples/NGS/tuxedo/tuxedo_no_novel_transcr.uwl +%%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 @@ -1222,7 +1400,6 @@ share/pixmaps/ugene.xpm %%DATADIR%%/workflow_samples/Scenarios/gene_by_gene_report.uwl %%DATADIR%%/workflow_samples/Scenarios/merge_sequence_annotation.uwl %%DATADIR%%/workflow_samples/Transcriptomics/SearchTFBS.uwl -%%DATADIR%%/workflow_samples/users/CreateAlignment.usa %%DATADIR%%/workflow_samples/users/Dump sequence info.usa %%DATADIR%%/workflow_samples/users/LinkData Fetch.usa %%DATADIR%%/workflow_samples/users/QualityFilter.usa @@ -1240,6 +1417,7 @@ share/pixmaps/ugene.xpm @dirrm %%DATADIR%%/workflow_samples/Alignment @dirrm %%DATADIR%%/workflow_samples @dirrm %%DATADIR%%/weight_matrix +@dirrm %%DATADIR%%/snp_scripts @dirrm %%DATADIR%%/sitecon_models/prokaryotic @dirrm %%DATADIR%%/sitecon_models/eukaryotic @dirrm %%DATADIR%%/sitecon_models @@ -1259,6 +1437,7 @@ share/pixmaps/ugene.xpm @dirrm %%DATADIR%%/samples/EMBL @dirrm %%DATADIR%%/samples/CLUSTALW @dirrm %%DATADIR%%/samples/Assembly +@dirrm %%DATADIR%%/samples/ACE @dirrm %%DATADIR%%/samples/ABIF @dirrm %%DATADIR%%/samples @dirrm %%DATADIR%%/query_samples @@ -1276,6 +1455,7 @@ share/pixmaps/ugene.xpm @dirrm %%DATADIR%%/position_weight_matrix/JASPAR/fungi @dirrm %%DATADIR%%/position_weight_matrix/JASPAR @dirrm %%DATADIR%%/position_weight_matrix +%%PORTDOCS%%@dirrm %%DOCSDIR%% @dirrm %%DATADIR%%/enzymes @dirrm %%DATADIR%%/cmdline @dirrm %%DATADIR%%/biostruct3d_plugin
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