svn commit: r339938 - in head/biology/ugene: . files
Alexey Dokuchaev
danfe at FreeBSD.org
Thu Jan 16 17:17:17 UTC 2014
Author: danfe
Date: Thu Jan 16 17:17:15 2014
New Revision: 339938
URL: http://svnweb.freebsd.org/changeset/ports/339938
QAT: https://qat.redports.org/buildarchive/r339938/
Log:
- Update to version 1.13.0 and improve FreeBSD support; it also builds
pretty cleanly with GCC v4.2, v4.6, and Clang (modulo a few warnings)
- Sadly, do not use PORTDOCS: since DOCSDIR is set to be inside DATADIR,
and will get appended to PLIST after @dirrm %%DATADIR%%, which upsets
sanity checking tools; instead, list the docs explicitly in DISTFILES
and add them to pkg-plist (guarded by %%PORTDOCS%%)
Tested on: i386 (only)
Added:
head/biology/ugene/files/patch-src-corelibs-U2Core-src-globals-AppResources.cpp (contents, props changed)
head/biology/ugene/files/patch-src-shtirlitz-Shtirlitz.cpp (contents, props changed)
head/biology/ugene/files/patch-src-ugenem-src-SendReportDialog.cpp (contents, props changed)
head/biology/ugene/files/patch-src-ugeneui-src-Main.cpp (contents, props changed)
Deleted:
head/biology/ugene/files/patch-clang-fixes
head/biology/ugene/files/patch-gtest-std::tr1::tuple-fix
Modified:
head/biology/ugene/Makefile
head/biology/ugene/distinfo
head/biology/ugene/pkg-plist
Modified: head/biology/ugene/Makefile
==============================================================================
--- head/biology/ugene/Makefile Thu Jan 16 17:16:10 2014 (r339937)
+++ head/biology/ugene/Makefile Thu Jan 16 17:17:15 2014 (r339938)
@@ -2,10 +2,11 @@
# $FreeBSD$
PORTNAME= ugene
-DISTVERSION= 1.12.3
+DISTVERSION= 1.13.0
CATEGORIES= biology
MASTER_SITES= http://ugene.unipro.ru/downloads/
-DISTFILES= ${DISTNAME}${EXTRACT_SUFX} ${PORTDOCS}
+DISTFILES= ${DISTNAME}${EXTRACT_SUFX} QueryDesigner_UserManual.pdf \
+ UniproUGENE_UserManual.pdf WorkflowDesigner_UserManual.pdf
DIST_SUBDIR= ${PORTNAME}
EXTRACT_ONLY= ${DISTNAME}${EXTRACT_SUFX}
@@ -22,7 +23,8 @@ RUN_DEPENDS= bash:${PORTSDIR}/shells/bas
USES= qmake
USE_GL= glu
USE_QT4= gui webkit xml svg linguist_build moc_build qmake_build \
- qtestlib_build rcc_build uic_build imageformats_run
+ qtestlib_build rcc_build uic_build imageformats_run \
+ scripttools_build
USE_XORG= xtst
USE_LDCONFIG= yes
INSTALLS_ICONS= yes
@@ -32,14 +34,13 @@ QMAKE_ARGS= INSTALL_PREFIX=${PREFIX} UGE
ALL_TARGET= release
DOCSDIR= ${DATADIR}/manuals
-PORTDOCS= QueryDesigner_UserManual.pdf UniproUGENE_UserManual.pdf \
- WorkflowDesigner_UserManual.pdf
OPTIONS_DEFINE= DOCS
DOCS_DESC= Install official UGENE documentation (PDF)
.include <bsd.port.pre.mk>
+# Required for Google Test code
.if ${OSVERSION} > 1000054
CXXFLAGS+= -std=c++11
.endif
@@ -64,10 +65,36 @@ post-patch:
@${REINPLACE_CMD} -e 's|/bin/bash|/usr/bin/env bash|' \
${WRKSRC}/src/gen_bin_script.cmd \
${WRKSRC}/installer/_common_data/ugene
-# remove BOM from files and non-latin comments; gcc 4.2 does not like them
- @${REINPLACE_CMD} -e '1s|^[^/]*|| ; /lose sequence view,/d' \
- ${WRKSRC}/src/plugins/GUITestBase/src/tests/common_scenarios/smith_waterman_dialog/GTTestsSWDialog.cpp \
- ${WRKSRC}/src/plugins/GUITestBase/src/tests/common_scenarios/repeat_finder/GTTestsRepeatFinder.cpp
+ @${REINPLACE_CMD} -e '30s|^|#include <time.h>|' \
+ ${WRKSRC}/src/plugins/dbi_bam/src/BAMDbiPlugin.h
+ @${REINPLACE_CMD} -e 's|runTime=NULL|runTime=0|' \
+ ${WRKSRC}/src/plugins/test_runner/src/TestViewReporter.h
+ @${REINPLACE_CMD} -e 's|Q_OS_LINUX|Q_OS_UNIX|' \
+ ${WRKSRC}/src/ugenem/src/main.cpp
+ @(cd ${WRKSRC}/src/plugins/external_tool_support/src && \
+ ${REINPLACE_CMD} -e 's/LINUX) || defined(Q_OS_MAC/UNIX/' \
+ ExternalToolSupportPlugin.cpp \
+ R/RSupport.cpp \
+ blast/BlastAllSupport.cpp \
+ blast/FormatDBSupport.cpp \
+ blast_plus/BlastDBCmdSupport.cpp \
+ blast_plus/BlastPlusSupport.cpp \
+ bowtie/BowtieSupport.cpp \
+ bowtie2/Bowtie2Support.cpp \
+ bwa/BwaSupport.cpp \
+ cap3/CAP3Support.cpp \
+ clustalo/ClustalOSupport.cpp \
+ clustalw/ClustalWSupport.cpp \
+ cufflinks/CufflinksSupport.cpp \
+ mrbayes/MrBayesSupport.cpp \
+ perl/PerlSupport.cpp \
+ python/PythonSupport.cpp \
+ samtools/BcfToolsSupport.cpp \
+ samtools/SamToolsExtToolSupport.cpp \
+ spidey/SpideySupport.cpp \
+ tcoffee/TCoffeeSupport.cpp \
+ tophat/TopHatSupport.cpp \
+ utils/ExternalToolSearchTask.cpp)
post-configure:
@${REINPLACE_CMD} -e '/^LFLAGS/s,-pthread,-lexecinfo &,' \
Modified: head/biology/ugene/distinfo
==============================================================================
--- head/biology/ugene/distinfo Thu Jan 16 17:16:10 2014 (r339937)
+++ head/biology/ugene/distinfo Thu Jan 16 17:17:15 2014 (r339938)
@@ -1,5 +1,5 @@
-SHA256 (ugene/ugene-1.12.3.tar.gz) = 6642ec6ef5110b50b38c9620be4a98101d9a7b325a61a202ee7e0f2c67d45496
-SIZE (ugene/ugene-1.12.3.tar.gz) = 17611949
+SHA256 (ugene/ugene-1.13.0.tar.gz) = 65bd8c343bb18a2aece4b0b9f703435727f1523b5a7344f43fe5e176b9428a3f
+SIZE (ugene/ugene-1.13.0.tar.gz) = 19079436
SHA256 (ugene/QueryDesigner_UserManual.pdf) = 3c5bd735c02b7ac24bd319823fde2d175b750adc1c37fe7b17e2009452a00ddd
SIZE (ugene/QueryDesigner_UserManual.pdf) = 1306825
SHA256 (ugene/UniproUGENE_UserManual.pdf) = 6c682c86f47a4c337eb4acdf0ae23ffa1b7fef1337d11e631655bfc943167b46
Added: head/biology/ugene/files/patch-src-corelibs-U2Core-src-globals-AppResources.cpp
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ head/biology/ugene/files/patch-src-corelibs-U2Core-src-globals-AppResources.cpp Thu Jan 16 17:17:15 2014 (r339938)
@@ -0,0 +1,73 @@
+--- src/corelibs/U2Core/src/globals/AppResources.cpp.orig
++++ src/corelibs/U2Core/src/globals/AppResources.cpp
+@@ -35,6 +35,10 @@
+ #include <proc/readproc.h>
+ #endif
+
++#if defined(Q_OS_LINUX) || defined(Q_OS_FREEBSD)
++#include <unistd.h> // for sysconf(3) and getpid(2)
++#endif
++
+ #ifdef Q_OS_WIN
+ #include <windows.h>
+ #include <Psapi.h>
+@@ -88,17 +92,15 @@ int AppResourcePool::getTotalPhysicalMem
+ coreLog.error("Total physical memory: getting info error");
+ }
+
+-#elif defined(Q_OS_LINUX)
+- QProcess p;
+- p.start("awk", QStringList() << "/MemTotal/ {print $2}" << "/proc/meminfo");
+- p.waitForFinished();
+- QString memory = p.readAllStandardOutput();
+- p.close();
+- bool ok = false;
+- qlonglong output_mem = memory.toLongLong(&ok);
+- if (ok) {
+- totalPhysicalMemory = output_mem / 1024;
+- }
++#elif defined(Q_OS_LINUX) || defined(Q_OS_FREEBSD)
++ long pagesize = sysconf(_SC_PAGESIZE);
++ long numpages = sysconf(_SC_PHYS_PAGES);
++
++ // Assume that page size is always a multiple of 1024, so it can be
++ // divided without losing any precision. On the other hand, number
++ // of pages would hardly overflow `long' when multiplied by a small
++ // number (number of pages / 1024), so we should be safe here.
++ totalPhysicalMemory = (int)(numpages * (pagesize / 1024) / 1024);
+
+ #elif defined(Q_OS_MAC)
+ // TODO
+@@ -143,15 +145,27 @@ void AppResourcePool::setMaxMemorySizeIn
+
+ size_t AppResourcePool::getCurrentAppMemory() {
+
+-#ifdef Q_OS_LINUX
+- struct proc_t usage;
+- //look_up_our_self(&usage);
+- return usage.vsize;
+-#endif
+ #ifdef Q_OS_WIN32
+ PROCESS_MEMORY_COUNTERS memCounter;
+ bool result = GetProcessMemoryInfo(GetCurrentProcess(), &memCounter, sizeof( memCounter ));
+ return memCounter.WorkingSetSize;
++#elif defined(Q_OS_LINUX)
++ struct proc_t usage;
++ //look_up_our_self(&usage);
++ return usage.vsize;
++#elif defined(Q_OS_FREEBSD)
++ QProcess p;
++ p.start("ps", QStringList() << "-o" << "vsize=" << "-p" << QString("%1").arg(getpid()));
++ p.waitForFinished();
++ QString ps_vsize = p.readAllStandardOutput();
++ p.close();
++ bool ok = false;
++ qlonglong output_mem = ps_vsize.toLongLong(&ok);
++ if (ok) {
++ return output_mem / 1024;
++ }
++#else
++ coreLog.error("Current application memory: Unsupported OS");
+ #endif
+ }
+
Added: head/biology/ugene/files/patch-src-shtirlitz-Shtirlitz.cpp
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ head/biology/ugene/files/patch-src-shtirlitz-Shtirlitz.cpp Thu Jan 16 17:17:15 2014 (r339938)
@@ -0,0 +1,14 @@
+--- src/ugeneui/src/shtirlitz/Shtirlitz.cpp.orig
++++ src/ugeneui/src/shtirlitz/Shtirlitz.cpp
+@@ -239,7 +239,10 @@ void Shtirlitz::getOsNameAndVersion( QSt
+ version = QString::number(QSysInfo::MacintoshVersion);
+ #elif defined(Q_OS_LINUX)
+ name = "Linux";
+- Q_UNUSED(version);//no version is available :(
++ Q_UNUSED(version); //no version is available :(
++#elif defined(Q_OS_FREEBSD)
++ name = "FreeBSD";
++ Q_UNUSED(version); //no version is available :(
+ #else
+ name = "Other";
+ #endif
Added: head/biology/ugene/files/patch-src-ugenem-src-SendReportDialog.cpp
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ head/biology/ugene/files/patch-src-ugenem-src-SendReportDialog.cpp Thu Jan 16 17:17:15 2014 (r339938)
@@ -0,0 +1,49 @@
+--- src/ugenem/src/SendReportDialog.cpp.orig
++++ src/ugenem/src/SendReportDialog.cpp
+@@ -44,6 +44,10 @@
+ #include <Winbase.h> //for IsProcessorFeaturePresent
+ #endif
+
++#if defined(Q_OS_LINUX) || defined(Q_OS_FREEBSD)
++#include <unistd.h> // for sysconf(3)
++#endif
++
+ #define HOST_URL "http://ugene.unipro.ru"
+ //#define HOST_URL "http://127.0.0.1"
+ #define DESTINATION_URL_KEEPER_PAGE "/crash_reports_dest.html"
+@@ -241,6 +245,8 @@ QString ReportSender::getOSVersion() {
+
+ #elif defined(Q_OS_LINUX)
+ result = "Linux";
++#elif defined(Q_OS_FREEBSD)
++ result = "FreeBSD";
+ #elif defined(Q_OS_MAC)
+ result = "Mac ";
+ switch (QSysInfo::MacintoshVersion){
+@@ -304,17 +310,15 @@ int ReportSender::getTotalPhysicalMemory
+ totalPhysicalMemory = memory_status.ullTotalPhys / (1024 * 1024);
+ }
+
+-#elif defined(Q_OS_LINUX)
+- QProcess p;
+- p.start("awk", QStringList() << "/MemTotal/ {print $2}" << "/proc/meminfo");
+- p.waitForFinished();
+- QString memory = p.readAllStandardOutput();
+- p.close();
+- bool ok = false;
+- qlonglong output_mem = memory.toLongLong(&ok);
+- if (ok) {
+- totalPhysicalMemory = output_mem / 1024;
+- }
++#elif defined(Q_OS_LINUX) || defined(Q_OS_FREEBSD)
++ long pagesize = sysconf(_SC_PAGESIZE);
++ long numpages = sysconf(_SC_PHYS_PAGES);
++
++ // Assume that page size is always a multiple of 1024, so it can be
++ // divided without losing any precision. On the other hand, number
++ // of pages would hardly overflow `long' when multiplied by a small
++ // number (number of pages / 1024), so we should be safe here.
++ totalPhysicalMemory = (int)(numpages * (pagesize / 1024) / 1024);
+
+ #elif defined(Q_OS_MAC)
+ // TODO
Added: head/biology/ugene/files/patch-src-ugeneui-src-Main.cpp
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ head/biology/ugene/files/patch-src-ugeneui-src-Main.cpp Thu Jan 16 17:17:15 2014 (r339938)
@@ -0,0 +1,20 @@
+--- src/ugeneui/src/Main.cpp.orig
++++ src/ugeneui/src/Main.cpp
+@@ -164,7 +164,7 @@ static void setDataSearchPaths() {
+ dataSearchPaths.push_back( appDirPath+RELATIVE_DEV_DATA_DIR );
+ }
+
+-#if (defined(Q_OS_LINUX) || defined(Q_OS_UNIX)) && defined( UGENE_DATA_DIR )
++#if defined(Q_OS_UNIX) && defined(UGENE_DATA_DIR)
+ //using directory which is set during installation process on Linux
+ QString ugene_data_dir( UGENE_DATA_DIR );
+ if( QDir(ugene_data_dir).exists() ) {
+@@ -361,7 +361,7 @@ int main(int argc, char **argv)
+ qt_use_native_dialogs = useNative; //using local here for debugger
+ #endif
+
+-#if defined(Q_OS_MAC) || defined(Q_OS_LINUX)
++#if defined(Q_OS_UNIX)
+ if (envList.indexOf("UGENE_GUI_TEST=1") >= 0) {
+ QApplication::setAttribute(Qt::AA_DontUseNativeMenuBar);
+ }
Modified: head/biology/ugene/pkg-plist
==============================================================================
--- head/biology/ugene/pkg-plist Thu Jan 16 17:16:10 2014 (r339937)
+++ head/biology/ugene/pkg-plist Thu Jan 16 17:17:15 2014 (r339938)
@@ -1,14 +1,48 @@
bin/ugene
lib/ugene/libU2Algorithm.so
+lib/ugene/libU2Algorithm.so.1
+lib/ugene/libU2Algorithm.so.1.0
+lib/ugene/libU2Algorithm.so.1.0.0
lib/ugene/libU2Core.so
+lib/ugene/libU2Core.so.1
+lib/ugene/libU2Core.so.1.0
+lib/ugene/libU2Core.so.1.0.0
lib/ugene/libU2Designer.so
+lib/ugene/libU2Designer.so.1
+lib/ugene/libU2Designer.so.1.0
+lib/ugene/libU2Designer.so.1.0.0
lib/ugene/libU2Formats.so
+lib/ugene/libU2Formats.so.1
+lib/ugene/libU2Formats.so.1.0
+lib/ugene/libU2Formats.so.1.0.0
lib/ugene/libU2Gui.so
+lib/ugene/libU2Gui.so.1
+lib/ugene/libU2Gui.so.1.0
+lib/ugene/libU2Gui.so.1.0.0
lib/ugene/libU2Lang.so
+lib/ugene/libU2Lang.so.1
+lib/ugene/libU2Lang.so.1.0
+lib/ugene/libU2Lang.so.1.0.0
lib/ugene/libU2Private.so
+lib/ugene/libU2Private.so.1
+lib/ugene/libU2Private.so.1.0
+lib/ugene/libU2Private.so.1.0.0
lib/ugene/libU2Remote.so
+lib/ugene/libU2Remote.so.1
+lib/ugene/libU2Remote.so.1.0
+lib/ugene/libU2Remote.so.1.0.0
+lib/ugene/libU2Script.so
+lib/ugene/libU2Script.so.1
+lib/ugene/libU2Script.so.1.0
+lib/ugene/libU2Script.so.1.0.0
lib/ugene/libU2Test.so
+lib/ugene/libU2Test.so.1
+lib/ugene/libU2Test.so.1.0
+lib/ugene/libU2Test.so.1.0.0
lib/ugene/libU2View.so
+lib/ugene/libU2View.so.1
+lib/ugene/libU2View.so.1.0
+lib/ugene/libU2View.so.1.0.0
lib/ugene/libgtest.so
lib/ugene/libgtest.so.1
lib/ugene/libgtest.so.1.0
@@ -18,8 +52,17 @@ lib/ugene/libugenedb.so.1
lib/ugene/libugenedb.so.1.0
lib/ugene/libugenedb.so.1.0.0
lib/ugene/plugins/libbrowser_support.so
+lib/ugene/plugins/libbrowser_support.so.1
+lib/ugene/plugins/libbrowser_support.so.1.0
+lib/ugene/plugins/libbrowser_support.so.1.0.0
lib/ugene/plugins/liblinkdata_support.so
+lib/ugene/plugins/liblinkdata_support.so.1
+lib/ugene/plugins/liblinkdata_support.so.1.0
+lib/ugene/plugins/liblinkdata_support.so.1.0.0
lib/ugene/plugins/libvariants.so
+lib/ugene/plugins/libvariants.so.1
+lib/ugene/plugins/libvariants.so.1.0
+lib/ugene/plugins/libvariants.so.1.0.0
lib/ugene/plugins/linkdata_support.license
lib/ugene/plugins/linkdata_support.plugin
lib/ugene/plugins/variants.license
@@ -69,43 +112,161 @@ lib/ugene/plugins/hmm2.plugin
lib/ugene/plugins/kalign.license
lib/ugene/plugins/kalign.plugin
lib/ugene/plugins/libCoreTests.so
+lib/ugene/plugins/libCoreTests.so.1
+lib/ugene/plugins/libCoreTests.so.1.0
+lib/ugene/plugins/libCoreTests.so.1.0.0
lib/ugene/plugins/libGUITestBase.so
+lib/ugene/plugins/libGUITestBase.so.1
+lib/ugene/plugins/libGUITestBase.so.1.0
+lib/ugene/plugins/libGUITestBase.so.1.0.0
lib/ugene/plugins/libannotator.so
+lib/ugene/plugins/libannotator.so.1
+lib/ugene/plugins/libannotator.so.1.0
+lib/ugene/plugins/libannotator.so.1.0.0
lib/ugene/plugins/libapi_tests.so
+lib/ugene/plugins/libapi_tests.so.1
+lib/ugene/plugins/libapi_tests.so.1.0
+lib/ugene/plugins/libapi_tests.so.1.0.0
lib/ugene/plugins/libball.so
+lib/ugene/plugins/libball.so.1
+lib/ugene/plugins/libball.so.1.0
+lib/ugene/plugins/libball.so.1.0.0
lib/ugene/plugins/libbiostruct3d_view.so
+lib/ugene/plugins/libbiostruct3d_view.so.1
+lib/ugene/plugins/libbiostruct3d_view.so.1.0
+lib/ugene/plugins/libbiostruct3d_view.so.1.0.0
lib/ugene/plugins/libchroma_view.so
+lib/ugene/plugins/libchroma_view.so.1
+lib/ugene/plugins/libchroma_view.so.1.0
+lib/ugene/plugins/libchroma_view.so.1.0.0
lib/ugene/plugins/libcircular_view.so
+lib/ugene/plugins/libcircular_view.so.1
+lib/ugene/plugins/libcircular_view.so.1.0
+lib/ugene/plugins/libcircular_view.so.1.0.0
lib/ugene/plugins/libdbi_bam.so
+lib/ugene/plugins/libdbi_bam.so.1
+lib/ugene/plugins/libdbi_bam.so.1.0
+lib/ugene/plugins/libdbi_bam.so.1.0.0
lib/ugene/plugins/libdna_export.so
+lib/ugene/plugins/libdna_export.so.1
+lib/ugene/plugins/libdna_export.so.1.0
+lib/ugene/plugins/libdna_export.so.1.0.0
lib/ugene/plugins/libdna_flexibility.so
+lib/ugene/plugins/libdna_flexibility.so.1
+lib/ugene/plugins/libdna_flexibility.so.1.0
+lib/ugene/plugins/libdna_flexibility.so.1.0.0
lib/ugene/plugins/libdna_graphpack.so
+lib/ugene/plugins/libdna_graphpack.so.1
+lib/ugene/plugins/libdna_graphpack.so.1.0
+lib/ugene/plugins/libdna_graphpack.so.1.0.0
lib/ugene/plugins/libdna_stat.so
+lib/ugene/plugins/libdna_stat.so.1
+lib/ugene/plugins/libdna_stat.so.1.0
+lib/ugene/plugins/libdna_stat.so.1.0.0
lib/ugene/plugins/libdotplot.so
+lib/ugene/plugins/libdotplot.so.1
+lib/ugene/plugins/libdotplot.so.1.0
+lib/ugene/plugins/libdotplot.so.1.0.0
lib/ugene/plugins/libenzymes.so
+lib/ugene/plugins/libenzymes.so.1
+lib/ugene/plugins/libenzymes.so.1.0
+lib/ugene/plugins/libenzymes.so.1.0.0
lib/ugene/plugins/libexpert_discovery.so
+lib/ugene/plugins/libexpert_discovery.so.1
+lib/ugene/plugins/libexpert_discovery.so.1.0
+lib/ugene/plugins/libexpert_discovery.so.1.0.0
lib/ugene/plugins/libexternal_tool_support.so
+lib/ugene/plugins/libexternal_tool_support.so.1
+lib/ugene/plugins/libexternal_tool_support.so.1.0
+lib/ugene/plugins/libexternal_tool_support.so.1.0.0
lib/ugene/plugins/libgenome_aligner.so
+lib/ugene/plugins/libgenome_aligner.so.1
+lib/ugene/plugins/libgenome_aligner.so.1.0
+lib/ugene/plugins/libgenome_aligner.so.1.0.0
lib/ugene/plugins/libgor4.so
+lib/ugene/plugins/libgor4.so.1
+lib/ugene/plugins/libgor4.so.1.0
+lib/ugene/plugins/libgor4.so.1.0.0
lib/ugene/plugins/libhmm2.so
+lib/ugene/plugins/libhmm2.so.1
+lib/ugene/plugins/libhmm2.so.1.0
+lib/ugene/plugins/libhmm2.so.1.0.0
lib/ugene/plugins/libkalign.so
+lib/ugene/plugins/libkalign.so.1
+lib/ugene/plugins/libkalign.so.1.0
+lib/ugene/plugins/libkalign.so.1.0.0
lib/ugene/plugins/libopencl_support.so
+lib/ugene/plugins/libopencl_support.so.1
+lib/ugene/plugins/libopencl_support.so.1.0
+lib/ugene/plugins/libopencl_support.so.1.0.0
lib/ugene/plugins/liborf_marker.so
+lib/ugene/plugins/liborf_marker.so.1
+lib/ugene/plugins/liborf_marker.so.1.0
+lib/ugene/plugins/liborf_marker.so.1.0.0
lib/ugene/plugins/libperf_monitor.so
+lib/ugene/plugins/libperf_monitor.so.1
+lib/ugene/plugins/libperf_monitor.so.1.0
+lib/ugene/plugins/libperf_monitor.so.1.0.0
lib/ugene/plugins/libphylip.so
+lib/ugene/plugins/libphylip.so.1
+lib/ugene/plugins/libphylip.so.1.0
+lib/ugene/plugins/libphylip.so.1.0.0
lib/ugene/plugins/libprimer3.so
+lib/ugene/plugins/libprimer3.so.1
+lib/ugene/plugins/libprimer3.so.1.0
+lib/ugene/plugins/libprimer3.so.1.0.0
lib/ugene/plugins/libpsipred.so
+lib/ugene/plugins/libpsipred.so.1
+lib/ugene/plugins/libpsipred.so.1.0
+lib/ugene/plugins/libpsipred.so.1.0.0
lib/ugene/plugins/libptools.so
+lib/ugene/plugins/libptools.so.1
+lib/ugene/plugins/libptools.so.1.0
+lib/ugene/plugins/libptools.so.1.0.0
lib/ugene/plugins/libquery_designer.so
+lib/ugene/plugins/libquery_designer.so.1
+lib/ugene/plugins/libquery_designer.so.1.0
+lib/ugene/plugins/libquery_designer.so.1.0.0
lib/ugene/plugins/libremote_blast.so
+lib/ugene/plugins/libremote_blast.so.1
+lib/ugene/plugins/libremote_blast.so.1.0
+lib/ugene/plugins/libremote_blast.so.1.0.0
lib/ugene/plugins/libremote_service.so
+lib/ugene/plugins/libremote_service.so.1
+lib/ugene/plugins/libremote_service.so.1.0
+lib/ugene/plugins/libremote_service.so.1.0.0
lib/ugene/plugins/librepeat_finder.so
+lib/ugene/plugins/librepeat_finder.so.1
+lib/ugene/plugins/librepeat_finder.so.1.0
+lib/ugene/plugins/librepeat_finder.so.1.0.0
lib/ugene/plugins/libsitecon.so
+lib/ugene/plugins/libsitecon.so.1
+lib/ugene/plugins/libsitecon.so.1.0
+lib/ugene/plugins/libsitecon.so.1.0.0
lib/ugene/plugins/libsmith_waterman.so
+lib/ugene/plugins/libsmith_waterman.so.1
+lib/ugene/plugins/libsmith_waterman.so.1.0
+lib/ugene/plugins/libsmith_waterman.so.1.0.0
+lib/ugene/plugins/libsnp_effect.so
+lib/ugene/plugins/libsnp_effect.so.1
+lib/ugene/plugins/libsnp_effect.so.1.0
+lib/ugene/plugins/libsnp_effect.so.1.0.0
lib/ugene/plugins/libtest_runner.so
+lib/ugene/plugins/libtest_runner.so.1
+lib/ugene/plugins/libtest_runner.so.1.0
+lib/ugene/plugins/libtest_runner.so.1.0.0
%%NOX64%%lib/ugene/plugins/libumuscle.so
+%%NOX64%%lib/ugene/plugins/libumuscle.so.1
+%%NOX64%%lib/ugene/plugins/libumuscle.so.1.0
+%%NOX64%%lib/ugene/plugins/libumuscle.so.1.0.0
lib/ugene/plugins/libweight_matrix.so
+lib/ugene/plugins/libweight_matrix.so.1
+lib/ugene/plugins/libweight_matrix.so.1.0
+lib/ugene/plugins/libweight_matrix.so.1.0.0
lib/ugene/plugins/libworkflow_designer.so
+lib/ugene/plugins/libworkflow_designer.so.1
+lib/ugene/plugins/libworkflow_designer.so.1.0
+lib/ugene/plugins/libworkflow_designer.so.1.0.0
lib/ugene/plugins/opencl_support.license
lib/ugene/plugins/opencl_support.plugin
lib/ugene/plugins/orf_marker.license
@@ -132,6 +293,8 @@ lib/ugene/plugins/sitecon.license
lib/ugene/plugins/sitecon.plugin
lib/ugene/plugins/smith_waterman.license
lib/ugene/plugins/smith_waterman.plugin
+lib/ugene/plugins/snp_effect.license
+lib/ugene/plugins/snp_effect.plugin
lib/ugene/plugins/test_runner.license
lib/ugene/plugins/test_runner.plugin
%%NOX64%%lib/ugene/plugins/umuscle.license
@@ -201,6 +364,7 @@ share/pixmaps/ugene.xpm
%%DATADIR%%/cmdline/align.uwl
%%DATADIR%%/cmdline/convert-msa.uwl
%%DATADIR%%/cmdline/convert-seq.uwl
+%%DATADIR%%/cmdline/das_annotation.uwl
%%DATADIR%%/cmdline/extract-sequence.uwl
%%DATADIR%%/cmdline/fetch-sequence.uwl
%%DATADIR%%/cmdline/find-orfs.uwl
@@ -222,8 +386,12 @@ share/pixmaps/ugene.xpm
%%DATADIR%%/cmdline/revcompl.uwl
%%DATADIR%%/cmdline/sitecon-build.uwl
%%DATADIR%%/cmdline/sitecon-search.uwl
+%%DATADIR%%/cmdline/snp.uwl
%%DATADIR%%/enzymes/2013_08_01.bairoch.gz
%%DATADIR%%/license
+%%PORTDOCS%%%%DOCSDIR%%/QueryDesigner_UserManual.pdf
+%%PORTDOCS%%%%DOCSDIR%%/UniproUGENE_UserManual.pdf
+%%PORTDOCS%%%%DOCSDIR%%/WorkflowDesigner_UserManual.pdf
%%DATADIR%%/position_weight_matrix/JASPAR/all_jaspar.csv
%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0265.1.pfm
%%DATADIR%%/position_weight_matrix/JASPAR/fungi/MA0266.1.pfm
@@ -973,6 +1141,8 @@ share/pixmaps/ugene.xpm
%%DATADIR%%/query_samples/RepeatsWithORF.uql
%%DATADIR%%/query_samples/SimpleGene.uql
%%DATADIR%%/samples/ABIF/A01.abi
+%%DATADIR%%/samples/ACE/K26.ace
+%%DATADIR%%/samples/ACE/BL060C3.ace
%%DATADIR%%/samples/Assembly/chrM.fa
%%DATADIR%%/samples/Assembly/chrM.sam
%%DATADIR%%/samples/Assembly/chrM.sorted.bam
@@ -1105,6 +1275,13 @@ share/pixmaps/ugene.xpm
%%DATADIR%%/sitecon_models/prokaryotic/TyrR.sitecon.gz
%%DATADIR%%/sitecon_models/prokaryotic/fis_new1.sitecon.gz
%%DATADIR%%/sitecon_models/prokaryotic/soxS.sitecon.gz
+%%DATADIR%%/snp_scripts/SNPChIPTools.py
+%%DATADIR%%/snp_scripts/pdb_uniprot_chain_map.lst.2
+%%DATADIR%%/snp_scripts/protstability1d.py
+%%DATADIR%%/snp_scripts/protstability3d.py
+%%DATADIR%%/snp_scripts/rsnp.py
+%%DATADIR%%/snp_scripts/snp2pdbsite.py
+%%DATADIR%%/snp_scripts/update_d_db.py
%%DATADIR%%/translations.txt
%%DATADIR%%/weight_matrix/blosum100.txt
%%DATADIR%%/weight_matrix/blosum30.txt
@@ -1195,7 +1372,6 @@ share/pixmaps/ugene.xpm
%%DATADIR%%/workflow_samples/Conversions/msa2clustal.uwl
%%DATADIR%%/workflow_samples/Conversions/query2alignment.uwl
%%DATADIR%%/workflow_samples/Conversions/seq2gen.uwl
-%%DATADIR%%/workflow_samples/Custom elements/script-create-alignment.uwl
%%DATADIR%%/workflow_samples/Custom elements/script-dump-sequence-info.uwl
%%DATADIR%%/workflow_samples/Custom elements/script-linkdata-fetch-seq.uwl
%%DATADIR%%/workflow_samples/Custom elements/script-quality-filter.uwl
@@ -1210,10 +1386,12 @@ share/pixmaps/ugene.xpm
%%DATADIR%%/workflow_samples/NGS/cistrome/chip_seq.uwl
%%DATADIR%%/workflow_samples/NGS/cistrome/chip_seq_with_control.uwl
%%DATADIR%%/workflow_samples/NGS/cistrome.uwl
+%%DATADIR%%/workflow_samples/NGS/consensus.uwl
+%%DATADIR%%/workflow_samples/NGS/extract_transcript_seq.uwl
%%DATADIR%%/workflow_samples/NGS/tuxedo/tuxedo_main.uwl
%%DATADIR%%/workflow_samples/NGS/tuxedo/tuxedo_main_paired.uwl
-%%DATADIR%%/workflow_samples/NGS/tuxedo/tuxedo_multiple_dataset.uwl
-%%DATADIR%%/workflow_samples/NGS/tuxedo/tuxedo_multiple_dataset_paired.uwl
+%%DATADIR%%/workflow_samples/NGS/tuxedo/tuxedo_no_novel_transcr.uwl
+%%DATADIR%%/workflow_samples/NGS/tuxedo/tuxedo_no_novel_transcr_paired.uwl
%%DATADIR%%/workflow_samples/NGS/tuxedo/tuxedo_single_dataset.uwl
%%DATADIR%%/workflow_samples/NGS/tuxedo/tuxedo_single_dataset_paired.uwl
%%DATADIR%%/workflow_samples/NGS/tuxedo.uwl
@@ -1222,7 +1400,6 @@ share/pixmaps/ugene.xpm
%%DATADIR%%/workflow_samples/Scenarios/gene_by_gene_report.uwl
%%DATADIR%%/workflow_samples/Scenarios/merge_sequence_annotation.uwl
%%DATADIR%%/workflow_samples/Transcriptomics/SearchTFBS.uwl
-%%DATADIR%%/workflow_samples/users/CreateAlignment.usa
%%DATADIR%%/workflow_samples/users/Dump sequence info.usa
%%DATADIR%%/workflow_samples/users/LinkData Fetch.usa
%%DATADIR%%/workflow_samples/users/QualityFilter.usa
@@ -1240,6 +1417,7 @@ share/pixmaps/ugene.xpm
@dirrm %%DATADIR%%/workflow_samples/Alignment
@dirrm %%DATADIR%%/workflow_samples
@dirrm %%DATADIR%%/weight_matrix
+ at 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
+ at dirrm %%DATADIR%%/samples/ACE
@dirrm %%DATADIR%%/samples/ABIF
@dirrm %%DATADIR%%/samples
@dirrm %%DATADIR%%/query_samples
@@ -1276,6 +1455,7 @@ share/pixmaps/ugene.xpm
@dirrm %%DATADIR%%/position_weight_matrix/JASPAR/fungi
@dirrm %%DATADIR%%/position_weight_matrix/JASPAR
@dirrm %%DATADIR%%/position_weight_matrix
+%%PORTDOCS%%@dirrm %%DOCSDIR%%
@dirrm %%DATADIR%%/enzymes
@dirrm %%DATADIR%%/cmdline
@dirrm %%DATADIR%%/biostruct3d_plugin
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