From c5854fe3e18c0fcd4b7873330008b39c2c5aa406 Mon Sep 17 00:00:00 2001 From: Alexey Dokuchaev Date: Thu, 31 Oct 2013 15:30:04 +0000 Subject: [PATCH] - Update to version 1.12.3 - Conditionalize dependency on `devel/libexecinfo' - Try to detect SSE2 support - Convert to USES=qmake and stafigy - Improve grammar in port description while here Approved by: maintainer (implicit) --- biology/ugene/Makefile | 41 +++-- biology/ugene/distinfo | 4 +- biology/ugene/files/patch-clang-fixes | 91 +++++++++ .../files/patch-gtest-std::tr1::tuple-fix | 34 ++++ ...rc-corelibs-U2Private-src-CrashHandler.cpp | 20 -- ...ns_3rdparty-umuscle-src-muscle-intmath.cpp | 30 --- biology/ugene/pkg-descr | 10 +- biology/ugene/pkg-plist | 174 +++++++++++++++++- 8 files changed, 325 insertions(+), 79 deletions(-) create mode 100644 biology/ugene/files/patch-clang-fixes create mode 100644 biology/ugene/files/patch-gtest-std::tr1::tuple-fix delete mode 100644 biology/ugene/files/patch-src-corelibs-U2Private-src-CrashHandler.cpp delete mode 100644 biology/ugene/files/patch-src-plugins_3rdparty-umuscle-src-muscle-intmath.cpp diff --git a/biology/ugene/Makefile b/biology/ugene/Makefile index 324afd10c12a..e1a7817c020f 100644 --- a/biology/ugene/Makefile +++ b/biology/ugene/Makefile @@ -2,7 +2,7 @@ # $FreeBSD$ PORTNAME= ugene -DISTVERSION= 1.11.4 +DISTVERSION= 1.12.3 CATEGORIES= biology MASTER_SITES= http://ugene.unipro.ru/downloads/ @@ -11,41 +11,54 @@ COMMENT= Free, open-source, cross-platform bioinformatics toolkit LICENSE= GPLv2 -LIB_DEPENDS= execinfo:${PORTSDIR}/devel/libexecinfo +.if !exists(/usr/include/execinfo.h) +LIB_DEPENDS= libexecinfo.so:${PORTSDIR}/devel/libexecinfo +.endif RUN_DEPENDS= bash:${PORTSDIR}/shells/bash +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 USE_XORG= xtst - USE_LDCONFIG= yes INSTALLS_ICONS= yes -MAN1= ${PORTNAME}.1 -MANCOMPRESSED= yes +QMAKE_ARGS= INSTALL_PREFIX=${PREFIX} UGENE_INSTALL_DATA=${DATADIR} \ + INSTALL_MANDIR=${MAN1PREFIX}/man +ALL_TARGET= release -NO_STAGE= yes .include +.if ${OSVERSION} > 1000054 +CXXFLAGS+= -std=c++11 +.endif + .if ${ARCH} == "amd64" -# need to manually tell the build we are on x64 -CARCH= CONFIG+=x64 +# XXX: need to manually tell the build we are on x64 +QMAKE_ARGS+= CONFIG+=x64 PLIST_SUB= NOX64="@comment " .else PLIST_SUB= NOX64="" .endif -# yes, bash is required, stuff will not execute with sh +.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 \ ${WRKSRC}/installer/_common_data/ugene +# remove BOM from files and non-latin comments; gcc 4.2 does not like them + @${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 -do-configure: - @cd ${CONFIGURE_WRKSRC} && ${SETENV} ${CONFIGURE_ENV} ${QMAKE} \ - PREFIX=${PREFIX} INSTALL_PREFIX=${PREFIX} \ - INSTALL_MANDIR=${MAN1PREFIX}/man ${CARCH} \ - UGENE_INSTALL_DATA=${DATADIR} -r ${PORTNAME}.pro +post-configure: + @${REINPLACE_CMD} -e '/^LFLAGS/s,-pthread,-lexecinfo &,' \ + ${WRKSRC}/src/ugenecl/Makefile.Release \ + ${WRKSRC}/src/ugeneui/Makefile.Release .include diff --git a/biology/ugene/distinfo b/biology/ugene/distinfo index 23b6433eef20..bad5b97da265 100644 --- a/biology/ugene/distinfo +++ b/biology/ugene/distinfo @@ -1,2 +1,2 @@ -SHA256 (ugene-1.11.4.tar.gz) = 5b9b914e7ef5a3d3658f3346cccdb5cd6583b03db3b7bed7e163cb5cfd5663fa -SIZE (ugene-1.11.4.tar.gz) = 14761290 +SHA256 (ugene-1.12.3.tar.gz) = 6642ec6ef5110b50b38c9620be4a98101d9a7b325a61a202ee7e0f2c67d45496 +SIZE (ugene-1.12.3.tar.gz) = 17611949 diff --git a/biology/ugene/files/patch-clang-fixes b/biology/ugene/files/patch-clang-fixes new file mode 100644 index 000000000000..3abf7b57fed1 --- /dev/null +++ b/biology/ugene/files/patch-clang-fixes @@ -0,0 +1,91 @@ +--- src/corelibs/U2Gui/src/util/ProjectTreeController.cpp.orig 2013-10-08 15:07:58.000000000 +0800 ++++ src/corelibs/U2Gui/src/util/ProjectTreeController.cpp 2013-10-30 19:47:27.000000000 +0800 +@@ -448,7 +448,7 @@ void ProjectTreeController::sl_onCloseEd + QMessageBox::critical(0, "Error", tr("Duplicate object names are not allowed")); + return; + +- } else if (newName.contains(invalidCharactersRegExp) != NULL) { ++ } else if (newName.contains(invalidCharactersRegExp) != false) { + QMessageBox::critical(0, "Error", tr("The name can't contain any of the following characters: %1").arg(invalidCharacters)); + return; + } +--- src/corelibs/U2Private/src/CrashHandler.cpp.orig 2013-10-08 15:07:59.000000000 +0800 ++++ src/corelibs/U2Private/src/CrashHandler.cpp 2013-10-30 19:18:30.000000000 +0800 +@@ -349,7 +349,7 @@ void CrashHandler::setupHandler() { + #define SA_FLAGS (SA_ONSTACK | SA_SIGINFO) + + stack_t sigstk; +- sigstk.ss_sp = malloc(SIGSTKSZ * 2); ++ sigstk.ss_sp = static_cast(malloc(SIGSTKSZ * 2)); + sigstk.ss_size = SIGSTKSZ * 2; + sigstk.ss_flags = 0; + if (sigaltstack(&sigstk,0) < 0) { +--- src/plugins/biostruct3d_view/src/MolecularSurfaceRenderer.cpp.orig 2013-10-08 15:07:39.000000000 +0800 ++++ src/plugins/biostruct3d_view/src/MolecularSurfaceRenderer.cpp 2013-10-30 21:42:54.000000000 +0800 +@@ -80,9 +80,21 @@ void DotsRenderer::drawSurface( Molecula + glBegin(GL_POINTS); + foreach(const Face& face, surface.getFaces()) { + float vct[3][3] = { +- {face.v[0].x,face.v[0].y,face.v[0].z}, +- {face.v[1].x,face.v[1].y,face.v[1].z}, +- {face.v[2].x,face.v[2].y,face.v[2].z}, ++ { ++ static_cast(face.v[0].x), ++ static_cast(face.v[0].y), ++ static_cast(face.v[0].z), ++ }, ++ { ++ static_cast(face.v[1].x), ++ static_cast(face.v[1].y), ++ static_cast(face.v[1].z), ++ }, ++ { ++ static_cast(face.v[2].x), ++ static_cast(face.v[2].y), ++ static_cast(face.v[2].z), ++ }, + }; + glVertex3fv(vct[0]); + glVertex3fv(vct[1]); +--- src/plugins/expert_discovery/src/ExpertDiscoveryTreeWidgetsCtrl.cpp.orig 2013-10-08 15:07:42.000000000 +0800 ++++ src/plugins/expert_discovery/src/ExpertDiscoveryTreeWidgetsCtrl.cpp 2013-10-30 22:02:40.000000000 +0800 +@@ -198,7 +198,7 @@ void EDProjectTree::updateSequenceBase(E + void EDProjectTree::sl_propChanged(EDProjectItem* item, const EDPIProperty* prop, QString newVal){ + switch (item->getType()) { + case PIT_CS_FOLDER: +- if (prop->getName().compare("Name", Qt::CaseInsensitive) == NULL) { ++ if (prop->getName().compare("Name", Qt::CaseInsensitive) == 0) { + EDPICSDirectory* pPI = dynamic_cast(item); + CSFolder* pFolder = findFolder(pPI); + const CSFolder* pParentFolder = pFolder->getParentFolder(); +--- src/plugins/test_runner/src/TestViewReporter.h.orig 2013-10-08 15:07:45.000000000 +0800 ++++ src/plugins/test_runner/src/TestViewReporter.h 2013-10-30 21:50:12.000000000 +0800 +@@ -44,7 +44,7 @@ namespace U2 { + + public: + +- TestViewReporter(TestViewController* parent,QTreeWidget* tree=NULL,int runTime=NULL); ++ TestViewReporter(TestViewController* parent,QTreeWidget* tree=NULL,int runTime=0); + QString getReportText() {return curReportText;} + bool saveAs(const QString url,const QString data); + +@@ -52,7 +52,7 @@ namespace U2 { + virtual void setupViewMenu(QMenu* n); + + private: +- const QString prepareHTMLText(QTreeWidget* tree=NULL,int runTime=NULL); ++ const QString prepareHTMLText(QTreeWidget* tree=NULL,int runTime=0); + + const QString getHTMLNoTests(); + const QString getHTMLHead(); +--- src/plugins_3rdparty/ball/src/source/COMMON/version.cpp.orig 2013-10-08 15:07:47.000000000 +0800 ++++ src/plugins_3rdparty/ball/src/source/COMMON/version.cpp 2013-10-30 21:20:22.000000000 +0800 +@@ -12,7 +12,7 @@ namespace BALL + { + const char* VersionInfo::getVersion() throw() + { +- return BALL_RELEASE_STRING " ("__DATE__", " __TIME__ ")"; ++ return BALL_RELEASE_STRING " (" __DATE__ ", " __TIME__ ")"; + } + + int VersionInfo::getMinorRevision() throw(Exception::InvalidFormat) diff --git a/biology/ugene/files/patch-gtest-std::tr1::tuple-fix b/biology/ugene/files/patch-gtest-std::tr1::tuple-fix new file mode 100644 index 000000000000..655f6c86d153 --- /dev/null +++ b/biology/ugene/files/patch-gtest-std::tr1::tuple-fix @@ -0,0 +1,34 @@ +commit 23699acca083589be9dc3b6e8e5c5d09f654648d +Author: marina.kolpakova +Date: Mon Oct 8 02:37:22 2012 +0400 + + fix for bug 2264 + + fix compilation OpenCV with cxx11 under Ubuntu with clang and gcc 4.7 + +diff --git a/modules/ts/include/opencv2/ts/ts_gtest.h b/modules/ts/include/opencv2/ts/ts_gtest.h +index f98f71b..42eb608 100644 +--- src/libs_3rdparty/gtest/src/gtest/internal/gtest-port.h.orig ++++ src/libs_3rdparty/gtest/src/gtest/internal/gtest-port.h +@@ -1654,7 +1654,21 @@ inline bool operator!=(const GTEST_10_TUPLE_(T)& t, + # undef _TR1_FUNCTIONAL // Allows the user to #include + // if he chooses to. + # else ++# if defined (__cplusplus) && __cplusplus > 199711L ++# include ++namespace std { ++ namespace tr1 { ++ using std::tuple; ++ using std::tuple_element; ++ using std::get; ++ using std::tuple_size; ++ using std::make_tuple; ++ } ++} ++# else + # include // NOLINT ++# endif ++ + # endif // !GTEST_HAS_RTTI && GTEST_GCC_VER_ < 40302 + + # else diff --git a/biology/ugene/files/patch-src-corelibs-U2Private-src-CrashHandler.cpp b/biology/ugene/files/patch-src-corelibs-U2Private-src-CrashHandler.cpp deleted file mode 100644 index 1e5e161bac43..000000000000 --- a/biology/ugene/files/patch-src-corelibs-U2Private-src-CrashHandler.cpp +++ /dev/null @@ -1,20 +0,0 @@ ---- ./src/corelibs/U2Private/src/CrashHandler.cpp.orig 2012-10-30 15:36:22.000000000 +0100 -+++ ./src/corelibs/U2Private/src/CrashHandler.cpp 2012-10-30 15:47:47.000000000 +0100 -@@ -253,7 +253,7 @@ - } - //handler = AddVectoredExceptionHandler(1, CrashHandlerFunc); - --#elif defined( Q_OS_MAC) -+#elif defined( Q_OS_MAC ) || defined ( Q_OS_FREEBSD ) - return; //TODO: implement crash hander for MAC OS - #else - stack_t sigstk; -@@ -284,7 +284,7 @@ - void CrashHandler::runMonitorProcess(const QString &exceptionType) { - QString path = QCoreApplication::applicationDirPath() + "/ugenem"; - --#ifndef Q_OS_WIN -+#if !defined ( Q_OS_WIN ) && !defined ( Q_OS_FREEBSD ) - char pid_buf[30]; - sprintf(pid_buf, "%d", getpid()); - char name_buf[512]; diff --git a/biology/ugene/files/patch-src-plugins_3rdparty-umuscle-src-muscle-intmath.cpp b/biology/ugene/files/patch-src-plugins_3rdparty-umuscle-src-muscle-intmath.cpp deleted file mode 100644 index f9f6d167af29..000000000000 --- a/biology/ugene/files/patch-src-plugins_3rdparty-umuscle-src-muscle-intmath.cpp +++ /dev/null @@ -1,30 +0,0 @@ ---- ./src/plugins_3rdparty/umuscle/src/muscle/intmath.cpp.orig 2012-12-26 17:43:44.000000000 +0800 -+++ ./src/plugins_3rdparty/umuscle/src/muscle/intmath.cpp 2013-02-25 17:25:06.000000000 +0800 -@@ -9,13 +9,6 @@ - return (PROB) pow(2.0, (double) Score/INTSCALE); - } - --static const double log2e = log2(exp(1.0)); -- --double lnTolog2(double ln) -- { -- return ln*log2e; -- } -- - double log2(double x) - { - if (0 == x) -@@ -27,6 +20,13 @@ - return log(x)*dInvLn2; - } - -+static const double log2e = log2(exp(1.0)); -+ -+double lnTolog2(double ln) -+ { -+ return ln*log2e; -+ } -+ - SCORE ProbToScore(PROB Prob) - { - if (0.0 == Prob) diff --git a/biology/ugene/pkg-descr b/biology/ugene/pkg-descr index 9ac1f2d9ce6d..a5e84919dfc2 100644 --- a/biology/ugene/pkg-descr +++ b/biology/ugene/pkg-descr @@ -1,12 +1,12 @@ -Unipro UGENE is a multiplatform open-source software with the main goal of +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 a common user interface. +manage, analyze, and visualize their data. UGENE integrates widely used +bioinformatics tools within one common user interface. -The toolkit supports multiple biological data formats and allows the +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. +phylogenetic trees, and 3D structures. WWW: http://ugene.unipro.ru/ diff --git a/biology/ugene/pkg-plist b/biology/ugene/pkg-plist index 39415697299c..e0f4ae7a6206 100644 --- a/biology/ugene/pkg-plist +++ b/biology/ugene/pkg-plist @@ -10,13 +10,28 @@ lib/ugene/libU2Remote.so lib/ugene/libU2Test.so lib/ugene/libU2View.so 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/libbrowser_support.so +lib/ugene/plugins/liblinkdata_support.so +lib/ugene/plugins/libvariants.so +lib/ugene/plugins/linkdata_support.license +lib/ugene/plugins/linkdata_support.plugin +lib/ugene/plugins/variants.license +lib/ugene/plugins/variants.plugin 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/browser_support.license +lib/ugene/plugins/browser_support.plugin lib/ugene/plugins/api_tests.license lib/ugene/plugins/api_tests.plugin lib/ugene/plugins/ball.license @@ -133,6 +148,7 @@ lib/ugene/ugene lib/ugene/ugenecl lib/ugene/ugenem lib/ugene/ugeneui +man/man1/ugene.1.gz share/applications/ugene.desktop share/pixmaps/ugene.png share/pixmaps/ugene.xpm @@ -177,21 +193,20 @@ share/pixmaps/ugene.xpm %%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.uwl -%%DATADIR%%/cmdline/bowtie-build.uwl -%%DATADIR%%/cmdline/bowtie.uwl %%DATADIR%%/cmdline/convert-msa.uwl %%DATADIR%%/cmdline/convert-seq.uwl %%DATADIR%%/cmdline/extract-sequence.uwl %%DATADIR%%/cmdline/fetch-sequence.uwl -%%DATADIR%%/cmdline/fetch.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 @@ -207,8 +222,7 @@ share/pixmaps/ugene.xpm %%DATADIR%%/cmdline/revcompl.uwl %%DATADIR%%/cmdline/sitecon-build.uwl %%DATADIR%%/cmdline/sitecon-search.uwl -%%DATADIR%%/enzymes/rebase_v003_all.bairoch.gz -%%DATADIR%%/enzymes/rebase_v003_t2_com.bairoch.gz +%%DATADIR%%/enzymes/2013_08_01.bairoch.gz %%DATADIR%%/license %%DATADIR%%/position_weight_matrix/JASPAR/all_jaspar.csv %%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0265.1.pfm @@ -389,6 +403,131 @@ share/pixmaps/ugene.xpm %%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0440.1.pfm %%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0441.1.pfm %%DATADIR%%/position_weight_matrix/JASPAR/fungi/matrix_list.txt +%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0010.1.pfm +%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0011.1.pfm +%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0012.1.pfm +%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0013.1.pfm +%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0015.1.pfm +%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0016.1.pfm +%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0022.1.pfm +%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0023.1.pfm +%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0026.1.pfm +%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA00445.1.pfm +%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0049.1.pfm +%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0085.1.pfm +%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0086.1.pfm +%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0094.2.pfm +%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0126.1.pfm +%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0165.1.pfm +%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0166.1.pfm +%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0167.1.pfm +%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0168.1.pfm +%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0169.1.pfm +%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0170.1.pfm +%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0171.1.pfm +%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0172.1.pfm +%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0173.1.pfm +%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0174.1.pfm +%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0175.1.pfm +%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0176.1.pfm +%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0177.1.pfm +%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0178.1.pfm +%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0179.1.pfm +%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0180.1.pfm +%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0181.1.pfm +%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0182.1.pfm +%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0183.1.pfm +%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0184.1.pfm +%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0185.1.pfm +%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0186.1.pfm +%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0187.1.pfm +%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0188.1.pfm +%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0189.1.pfm +%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0190.1.pfm +%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0191.1.pfm +%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0192.1.pfm +%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0193.1.pfm +%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0194.1.pfm +%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0195.1.pfm +%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0196.1.pfm +%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0197.1.pfm +%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0198.1.pfm +%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0199.1.pfm +%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0200.1.pfm +%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0201.1.pfm +%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0202.1.pfm +%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0203.1.pfm +%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0204.1.pfm +%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0205.1.pfm +%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0206.1.pfm +%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0207.1.pfm +%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0208.1.pfm +%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0209.1.pfm +%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0210.1.pfm +%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0211.1.pfm +%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0212.1.pfm +%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0213.1.pfm +%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0214.1.pfm +%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0215.1.pfm +%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0216.1.pfm +%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0217.1.pfm +%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0218.1.pfm +%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0219.1.pfm +%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0220.1.pfm +%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0221.1.pfm +%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0222.1.pfm +%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0223.1.pfm +%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0224.1.pfm +%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0225.1.pfm +%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0226.1.pfm +%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0227.1.pfm +%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0228.1.pfm +%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0229.1.pfm +%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0230.1.pfm +%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0231.1.pfm +%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0232.1.pfm +%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0233.1.pfm +%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0234.1.pfm +%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0235.1.pfm +%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0236.1.pfm +%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0237.1.pfm +%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0238.1.pfm +%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0239.1.pfm +%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0240.1.pfm +%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0241.1.pfm +%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0242.1.pfm +%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0243.1.pfm +%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0244.1.pfm +%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0245.1.pfm +%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0246.1.pfm +%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0247.1.pfm +%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0248.1.pfm +%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0249.1.pfm +%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0250.1.pfm +%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0251.1.pfm +%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0252.1.pfm +%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0253.1.pfm +%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0254.1.pfm +%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0255.1.pfm +%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0256.1.pfm +%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0257.1.pfm +%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0443.1.pfm +%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0444.1.pfm +%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0446.1.pfm +%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0447.1.pfm +%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0448.1.pfm +%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0449.1.pfm +%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0450.1.pfm +%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0451.1.pfm +%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0452.1.pfm +%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0453.1.pfm +%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0454.1.pfm +%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0455.1.pfm +%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0456.1.pfm +%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0457.1.pfm +%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0458.1.pfm +%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0459.1.pfm +%%DATADIR%%/position_weight_matrix/JASPAR/insects/MA0460.1.pfm %%DATADIR%%/position_weight_matrix/JASPAR/insects/matrix_list.txt %%DATADIR%%/position_weight_matrix/JASPAR/nematodes/MA0260.1.pfm %%DATADIR%%/position_weight_matrix/JASPAR/nematodes/MA0261.1.pfm @@ -834,8 +973,6 @@ share/pixmaps/ugene.xpm %%DATADIR%%/query_samples/RepeatsWithORF.uql %%DATADIR%%/query_samples/SimpleGene.uql %%DATADIR%%/samples/ABIF/A01.abi -%%DATADIR%%/samples/ACE/BL060C3.ace -%%DATADIR%%/samples/ACE/K26.ace %%DATADIR%%/samples/Assembly/chrM.fa %%DATADIR%%/samples/Assembly/chrM.sam %%DATADIR%%/samples/Assembly/chrM.sorted.bam @@ -1058,7 +1195,9 @@ 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 %%DATADIR%%/workflow_samples/Data marking/annotation_marker.uwl %%DATADIR%%/workflow_samples/Data marking/length_marker.uwl @@ -1067,12 +1206,32 @@ 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/call_variants.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/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_single_dataset.uwl +%%DATADIR%%/workflow_samples/NGS/tuxedo/tuxedo_single_dataset_paired.uwl +%%DATADIR%%/workflow_samples/NGS/tuxedo.uwl +%%DATADIR%%/workflow_samples/Scenarios/filter_matched.uwl +%%DATADIR%%/workflow_samples/Scenarios/find_sequences.uwl +%%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 @dirrm %%DATADIR%%/workflow_samples/users @dirrm %%DATADIR%%/workflow_samples/Transcriptomics +@dirrm %%DATADIR%%/workflow_samples/Scenarios +@dirrm %%DATADIR%%/workflow_samples/NGS/tuxedo +@dirrm %%DATADIR%%/workflow_samples/NGS/cistrome +@dirrm %%DATADIR%%/workflow_samples/NGS @dirrm %%DATADIR%%/workflow_samples/HMMER @dirrm %%DATADIR%%/workflow_samples/Data merging @dirrm %%DATADIR%%/workflow_samples/Data marking @@ -1100,7 +1259,6 @@ 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