- 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)
This commit is contained in:
parent
ff86bdb0ba
commit
c5854fe3e1
Notes:
svn2git
2021-03-31 03:12:20 +00:00
svn path=/head/; revision=332256
8 changed files with 325 additions and 79 deletions
|
@ -2,7 +2,7 @@
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# $FreeBSD$
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PORTNAME= ugene
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DISTVERSION= 1.11.4
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DISTVERSION= 1.12.3
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CATEGORIES= biology
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MASTER_SITES= http://ugene.unipro.ru/downloads/
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@ -11,41 +11,54 @@ COMMENT= Free, open-source, cross-platform bioinformatics toolkit
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LICENSE= GPLv2
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LIB_DEPENDS= execinfo:${PORTSDIR}/devel/libexecinfo
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.if !exists(/usr/include/execinfo.h)
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LIB_DEPENDS= libexecinfo.so:${PORTSDIR}/devel/libexecinfo
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.endif
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RUN_DEPENDS= bash:${PORTSDIR}/shells/bash
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USES= qmake
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USE_GL= glu
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USE_QT4= gui webkit xml svg linguist_build moc_build qmake_build \
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qtestlib_build rcc_build uic_build imageformats_run
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USE_XORG= xtst
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USE_LDCONFIG= yes
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INSTALLS_ICONS= yes
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MAN1= ${PORTNAME}.1
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MANCOMPRESSED= yes
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QMAKE_ARGS= INSTALL_PREFIX=${PREFIX} UGENE_INSTALL_DATA=${DATADIR} \
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INSTALL_MANDIR=${MAN1PREFIX}/man
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ALL_TARGET= release
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NO_STAGE= yes
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.include <bsd.port.pre.mk>
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.if ${OSVERSION} > 1000054
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CXXFLAGS+= -std=c++11
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.endif
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.if ${ARCH} == "amd64"
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# need to manually tell the build we are on x64
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CARCH= CONFIG+=x64
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# XXX: need to manually tell the build we are on x64
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QMAKE_ARGS+= CONFIG+=x64
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PLIST_SUB= NOX64="@comment "
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.else
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PLIST_SUB= NOX64=""
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.endif
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# yes, bash is required, stuff will not execute with sh
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.if ${MACHINE_CPU:Msse2}
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QMAKE_ARGS+= UGENE_SSE2_DETECTED=1
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.endif
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post-patch:
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# yes, bash is required, stuff will not execute with sh
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@${REINPLACE_CMD} -e 's|/bin/bash|/usr/bin/env bash|' \
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${WRKSRC}/src/gen_bin_script.cmd \
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${WRKSRC}/installer/_common_data/ugene
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# remove BOM from files and non-latin comments; gcc 4.2 does not like them
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@${REINPLACE_CMD} -e '1s|^[^/]*|| ; /lose sequence view,/d' \
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${WRKSRC}/src/plugins/GUITestBase/src/tests/common_scenarios/smith_waterman_dialog/GTTestsSWDialog.cpp \
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${WRKSRC}/src/plugins/GUITestBase/src/tests/common_scenarios/repeat_finder/GTTestsRepeatFinder.cpp
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do-configure:
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@cd ${CONFIGURE_WRKSRC} && ${SETENV} ${CONFIGURE_ENV} ${QMAKE} \
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PREFIX=${PREFIX} INSTALL_PREFIX=${PREFIX} \
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INSTALL_MANDIR=${MAN1PREFIX}/man ${CARCH} \
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UGENE_INSTALL_DATA=${DATADIR} -r ${PORTNAME}.pro
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post-configure:
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@${REINPLACE_CMD} -e '/^LFLAGS/s,-pthread,-lexecinfo &,' \
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${WRKSRC}/src/ugenecl/Makefile.Release \
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${WRKSRC}/src/ugeneui/Makefile.Release
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.include <bsd.port.post.mk>
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|
|
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@ -1,2 +1,2 @@
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SHA256 (ugene-1.11.4.tar.gz) = 5b9b914e7ef5a3d3658f3346cccdb5cd6583b03db3b7bed7e163cb5cfd5663fa
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SIZE (ugene-1.11.4.tar.gz) = 14761290
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SHA256 (ugene-1.12.3.tar.gz) = 6642ec6ef5110b50b38c9620be4a98101d9a7b325a61a202ee7e0f2c67d45496
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SIZE (ugene-1.12.3.tar.gz) = 17611949
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|
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91
biology/ugene/files/patch-clang-fixes
Normal file
91
biology/ugene/files/patch-clang-fixes
Normal file
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@ -0,0 +1,91 @@
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--- src/corelibs/U2Gui/src/util/ProjectTreeController.cpp.orig 2013-10-08 15:07:58.000000000 +0800
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+++ src/corelibs/U2Gui/src/util/ProjectTreeController.cpp 2013-10-30 19:47:27.000000000 +0800
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@@ -448,7 +448,7 @@ void ProjectTreeController::sl_onCloseEd
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QMessageBox::critical(0, "Error", tr("Duplicate object names are not allowed"));
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return;
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- } else if (newName.contains(invalidCharactersRegExp) != NULL) {
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+ } else if (newName.contains(invalidCharactersRegExp) != false) {
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QMessageBox::critical(0, "Error", tr("The name can't contain any of the following characters: %1").arg(invalidCharacters));
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return;
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}
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--- src/corelibs/U2Private/src/CrashHandler.cpp.orig 2013-10-08 15:07:59.000000000 +0800
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+++ src/corelibs/U2Private/src/CrashHandler.cpp 2013-10-30 19:18:30.000000000 +0800
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@@ -349,7 +349,7 @@ void CrashHandler::setupHandler() {
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#define SA_FLAGS (SA_ONSTACK | SA_SIGINFO)
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stack_t sigstk;
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- sigstk.ss_sp = malloc(SIGSTKSZ * 2);
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+ sigstk.ss_sp = static_cast<char *>(malloc(SIGSTKSZ * 2));
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sigstk.ss_size = SIGSTKSZ * 2;
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sigstk.ss_flags = 0;
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if (sigaltstack(&sigstk,0) < 0) {
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--- src/plugins/biostruct3d_view/src/MolecularSurfaceRenderer.cpp.orig 2013-10-08 15:07:39.000000000 +0800
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+++ src/plugins/biostruct3d_view/src/MolecularSurfaceRenderer.cpp 2013-10-30 21:42:54.000000000 +0800
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@@ -80,9 +80,21 @@ void DotsRenderer::drawSurface( Molecula
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glBegin(GL_POINTS);
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foreach(const Face& face, surface.getFaces()) {
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float vct[3][3] = {
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- {face.v[0].x,face.v[0].y,face.v[0].z},
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- {face.v[1].x,face.v[1].y,face.v[1].z},
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- {face.v[2].x,face.v[2].y,face.v[2].z},
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+ {
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+ static_cast<float>(face.v[0].x),
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+ static_cast<float>(face.v[0].y),
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+ static_cast<float>(face.v[0].z),
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+ },
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+ {
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+ static_cast<float>(face.v[1].x),
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+ static_cast<float>(face.v[1].y),
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+ static_cast<float>(face.v[1].z),
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+ },
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+ {
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+ static_cast<float>(face.v[2].x),
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+ static_cast<float>(face.v[2].y),
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+ static_cast<float>(face.v[2].z),
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+ },
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};
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glVertex3fv(vct[0]);
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glVertex3fv(vct[1]);
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--- src/plugins/expert_discovery/src/ExpertDiscoveryTreeWidgetsCtrl.cpp.orig 2013-10-08 15:07:42.000000000 +0800
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+++ src/plugins/expert_discovery/src/ExpertDiscoveryTreeWidgetsCtrl.cpp 2013-10-30 22:02:40.000000000 +0800
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@@ -198,7 +198,7 @@ void EDProjectTree::updateSequenceBase(E
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void EDProjectTree::sl_propChanged(EDProjectItem* item, const EDPIProperty* prop, QString newVal){
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switch (item->getType()) {
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case PIT_CS_FOLDER:
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- if (prop->getName().compare("Name", Qt::CaseInsensitive) == NULL) {
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+ if (prop->getName().compare("Name", Qt::CaseInsensitive) == 0) {
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EDPICSDirectory* pPI = dynamic_cast<EDPICSDirectory*>(item);
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CSFolder* pFolder = findFolder(pPI);
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const CSFolder* pParentFolder = pFolder->getParentFolder();
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--- src/plugins/test_runner/src/TestViewReporter.h.orig 2013-10-08 15:07:45.000000000 +0800
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+++ src/plugins/test_runner/src/TestViewReporter.h 2013-10-30 21:50:12.000000000 +0800
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@@ -44,7 +44,7 @@ namespace U2 {
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public:
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- TestViewReporter(TestViewController* parent,QTreeWidget* tree=NULL,int runTime=NULL);
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+ TestViewReporter(TestViewController* parent,QTreeWidget* tree=NULL,int runTime=0);
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QString getReportText() {return curReportText;}
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bool saveAs(const QString url,const QString data);
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@@ -52,7 +52,7 @@ namespace U2 {
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virtual void setupViewMenu(QMenu* n);
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private:
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- const QString prepareHTMLText(QTreeWidget* tree=NULL,int runTime=NULL);
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+ const QString prepareHTMLText(QTreeWidget* tree=NULL,int runTime=0);
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const QString getHTMLNoTests();
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const QString getHTMLHead();
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--- src/plugins_3rdparty/ball/src/source/COMMON/version.cpp.orig 2013-10-08 15:07:47.000000000 +0800
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+++ src/plugins_3rdparty/ball/src/source/COMMON/version.cpp 2013-10-30 21:20:22.000000000 +0800
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@@ -12,7 +12,7 @@ namespace BALL
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{
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const char* VersionInfo::getVersion() throw()
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{
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- return BALL_RELEASE_STRING " ("__DATE__", " __TIME__ ")";
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+ return BALL_RELEASE_STRING " (" __DATE__ ", " __TIME__ ")";
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}
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|
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int VersionInfo::getMinorRevision() throw(Exception::InvalidFormat)
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34
biology/ugene/files/patch-gtest-std::tr1::tuple-fix
Normal file
34
biology/ugene/files/patch-gtest-std::tr1::tuple-fix
Normal file
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@ -0,0 +1,34 @@
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commit 23699acca083589be9dc3b6e8e5c5d09f654648d
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Author: marina.kolpakova <marina.kolpakova@itseez.com>
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Date: Mon Oct 8 02:37:22 2012 +0400
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fix for bug 2264
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fix compilation OpenCV with cxx11 under Ubuntu with clang and gcc 4.7
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diff --git a/modules/ts/include/opencv2/ts/ts_gtest.h b/modules/ts/include/opencv2/ts/ts_gtest.h
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index f98f71b..42eb608 100644
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--- src/libs_3rdparty/gtest/src/gtest/internal/gtest-port.h.orig
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+++ src/libs_3rdparty/gtest/src/gtest/internal/gtest-port.h
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@@ -1654,7 +1654,21 @@ inline bool operator!=(const GTEST_10_TUPLE_(T)& t,
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# undef _TR1_FUNCTIONAL // Allows the user to #include
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// <tr1/functional> if he chooses to.
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# else
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+# if defined (__cplusplus) && __cplusplus > 199711L
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+# include <tuple>
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+namespace std {
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+ namespace tr1 {
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+ using std::tuple;
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+ using std::tuple_element;
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+ using std::get;
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+ using std::tuple_size;
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+ using std::make_tuple;
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+ }
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+}
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+# else
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# include <tr1/tuple> // NOLINT
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+# endif
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+
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# endif // !GTEST_HAS_RTTI && GTEST_GCC_VER_ < 40302
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# else
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@ -1,20 +0,0 @@
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--- ./src/corelibs/U2Private/src/CrashHandler.cpp.orig 2012-10-30 15:36:22.000000000 +0100
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+++ ./src/corelibs/U2Private/src/CrashHandler.cpp 2012-10-30 15:47:47.000000000 +0100
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@@ -253,7 +253,7 @@
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}
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//handler = AddVectoredExceptionHandler(1, CrashHandlerFunc);
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-#elif defined( Q_OS_MAC)
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+#elif defined( Q_OS_MAC ) || defined ( Q_OS_FREEBSD )
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return; //TODO: implement crash hander for MAC OS
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#else
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stack_t sigstk;
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@@ -284,7 +284,7 @@
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void CrashHandler::runMonitorProcess(const QString &exceptionType) {
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QString path = QCoreApplication::applicationDirPath() + "/ugenem";
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|
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-#ifndef Q_OS_WIN
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+#if !defined ( Q_OS_WIN ) && !defined ( Q_OS_FREEBSD )
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char pid_buf[30];
|
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sprintf(pid_buf, "%d", getpid());
|
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char name_buf[512];
|
|
@ -1,30 +0,0 @@
|
|||
--- ./src/plugins_3rdparty/umuscle/src/muscle/intmath.cpp.orig 2012-12-26 17:43:44.000000000 +0800
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+++ ./src/plugins_3rdparty/umuscle/src/muscle/intmath.cpp 2013-02-25 17:25:06.000000000 +0800
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@@ -9,13 +9,6 @@
|
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return (PROB) pow(2.0, (double) Score/INTSCALE);
|
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}
|
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|
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-static const double log2e = log2(exp(1.0));
|
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-
|
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-double lnTolog2(double ln)
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- {
|
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- return ln*log2e;
|
||||
- }
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-
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double log2(double x)
|
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{
|
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if (0 == x)
|
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@@ -27,6 +20,13 @@
|
||||
return log(x)*dInvLn2;
|
||||
}
|
||||
|
||||
+static const double log2e = log2(exp(1.0));
|
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+
|
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+double lnTolog2(double ln)
|
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+ {
|
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+ return ln*log2e;
|
||||
+ }
|
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+
|
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SCORE ProbToScore(PROB Prob)
|
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{
|
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if (0.0 == Prob)
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|
@ -1,12 +1,12 @@
|
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Unipro UGENE is a multiplatform open-source software with the main goal of
|
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Unipro UGENE is multiplatform, open-source software with the main goal of
|
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assisting molecular biologists without much expertise in bioinformatics to
|
||||
manage, analyze and visualize their data. UGENE integrates widely used
|
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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/
|
||||
|
|
|
@ -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
|
||||
|
|
Loading…
Reference in a new issue