Date: Thu, 31 Oct 2013 15:30:04 +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: r332256 - in head/biology/ugene: . files Message-ID: <201310311530.r9VFU4SG043746@svn.freebsd.org>
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Author: danfe Date: Thu Oct 31 15:30:04 2013 New Revision: 332256 URL: http://svnweb.freebsd.org/changeset/ports/332256 Log: - 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) Added: head/biology/ugene/files/patch-clang-fixes (contents, props changed) head/biology/ugene/files/patch-gtest-std::tr1::tuple-fix (contents, props changed) Deleted: head/biology/ugene/files/patch-src-corelibs-U2Private-src-CrashHandler.cpp head/biology/ugene/files/patch-src-plugins_3rdparty-umuscle-src-muscle-intmath.cpp Modified: head/biology/ugene/Makefile head/biology/ugene/distinfo head/biology/ugene/pkg-descr head/biology/ugene/pkg-plist Modified: head/biology/ugene/Makefile ============================================================================== --- head/biology/ugene/Makefile Thu Oct 31 15:25:09 2013 (r332255) +++ head/biology/ugene/Makefile Thu Oct 31 15:30:04 2013 (r332256) @@ -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-platfo 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 <bsd.port.pre.mk> +.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 - -do-configure: - @cd ${CONFIGURE_WRKSRC} && ${SETENV} ${CONFIGURE_ENV} ${QMAKE} \ - PREFIX=${PREFIX} INSTALL_PREFIX=${PREFIX} \ - INSTALL_MANDIR=${MAN1PREFIX}/man ${CARCH} \ - UGENE_INSTALL_DATA=${DATADIR} -r ${PORTNAME}.pro +# remove BOM from files and non-latin comments; gcc 4.2 does not like them + @${REINPLACE_CMD} -e '1s|^[^/]*|| ; /lose sequence view,/d' \ + ${WRKSRC}/src/plugins/GUITestBase/src/tests/common_scenarios/smith_waterman_dialog/GTTestsSWDialog.cpp \ + ${WRKSRC}/src/plugins/GUITestBase/src/tests/common_scenarios/repeat_finder/GTTestsRepeatFinder.cpp + +post-configure: + @${REINPLACE_CMD} -e '/^LFLAGS/s,-pthread,-lexecinfo &,' \ + ${WRKSRC}/src/ugenecl/Makefile.Release \ + ${WRKSRC}/src/ugeneui/Makefile.Release .include <bsd.port.post.mk> Modified: head/biology/ugene/distinfo ============================================================================== --- head/biology/ugene/distinfo Thu Oct 31 15:25:09 2013 (r332255) +++ head/biology/ugene/distinfo Thu Oct 31 15:30:04 2013 (r332256) @@ -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 Added: head/biology/ugene/files/patch-clang-fixes ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/ugene/files/patch-clang-fixes Thu Oct 31 15:30:04 2013 (r332256) @@ -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<char *>(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<float>(face.v[0].x), ++ static_cast<float>(face.v[0].y), ++ static_cast<float>(face.v[0].z), ++ }, ++ { ++ static_cast<float>(face.v[1].x), ++ static_cast<float>(face.v[1].y), ++ static_cast<float>(face.v[1].z), ++ }, ++ { ++ static_cast<float>(face.v[2].x), ++ static_cast<float>(face.v[2].y), ++ static_cast<float>(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<EDPICSDirectory*>(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) Added: head/biology/ugene/files/patch-gtest-std::tr1::tuple-fix ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/ugene/files/patch-gtest-std::tr1::tuple-fix Thu Oct 31 15:30:04 2013 (r332256) @@ -0,0 +1,34 @@ +commit 23699acca083589be9dc3b6e8e5c5d09f654648d +Author: marina.kolpakova <marina.kolpakova@itseez.com> +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 + // <tr1/functional> if he chooses to. + # else ++# if defined (__cplusplus) && __cplusplus > 199711L ++# include <tuple> ++namespace std { ++ namespace tr1 { ++ using std::tuple; ++ using std::tuple_element; ++ using std::get; ++ using std::tuple_size; ++ using std::make_tuple; ++ } ++} ++# else + # include <tr1/tuple> // NOLINT ++# endif ++ + # endif // !GTEST_HAS_RTTI && GTEST_GCC_VER_ < 40302 + + # else Modified: head/biology/ugene/pkg-descr ============================================================================== --- head/biology/ugene/pkg-descr Thu Oct 31 15:25:09 2013 (r332255) +++ head/biology/ugene/pkg-descr Thu Oct 31 15:30:04 2013 (r332256) @@ -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/ Modified: head/biology/ugene/pkg-plist ============================================================================== --- head/biology/ugene/pkg-plist Thu Oct 31 15:25:09 2013 (r332255) +++ head/biology/ugene/pkg-plist Thu Oct 31 15:30:04 2013 (r332256) @@ -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
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