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Code Issues Releases Activity

- Update to version 1.13.0 and improve FreeBSD support; it also builds

Browse Source 
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)
This commit is contained in:
Alexey Dokuchaev 2014-01-16 17:17:15 +00:00
parent adac2a3665
commit 9dc680d0e8
Notes: svn2git 2021-03-31 03:12:20 +00:00 
svn path=/head/; revision=339938
9 changed files with 378 additions and 140 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

45
biology/ugene/Makefile
View File

@ -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:${PORTSDIR}/shells/bash
USES= qmake
USE_GL= glu
USE_QT4= gui webkit xml svg linguist_build moc_build qmake_build \
qtestlib_build rcc_build uic_build imageformats_run
qtestlib_build rcc_build uic_build imageformats_run \
scripttools_build
USE_XORG= xtst
USE_LDCONFIG= yes
INSTALLS_ICONS= yes
@ -32,14 +34,13 @@ QMAKE_ARGS= INSTALL_PREFIX=${PREFIX} UGENE_INSTALL_DATA=${DATADIR} \
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 &,' \

4
biology/ugene/distinfo
View File

@ -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

91
biology/ugene/files/patch-clang-fixes
View File

@ -1,91 +0,0 @@
--- 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)

34
biology/ugene/files/patch-gtest-std::tr1::tuple-fix
View File

@ -1,34 +0,0 @@
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

73
biology/ugene/files/patch-src-corelibs-U2Core-src-globals-AppResources.cpp Normal file
View File

@ -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
}

14
biology/ugene/files/patch-src-shtirlitz-Shtirlitz.cpp Normal file
View File

@ -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

49
biology/ugene/files/patch-src-ugenem-src-SendReportDialog.cpp Normal file
View File

@ -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

20
biology/ugene/files/patch-src-ugeneui-src-Main.cpp Normal file
View File

@ -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);
}

188
biology/ugene/pkg-plist
View File

@ -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
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lib/ugene/plugins/libexternal_tool_support.so
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lib/ugene/plugins/libgenome_aligner.so
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lib/ugene/plugins/libhmm2.so
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lib/ugene/plugins/libkalign.so
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lib/ugene/plugins/libphylip.so
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lib/ugene/plugins/libpsipred.so
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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