diff options
| -rw-r--r-- | biology/ugene/Makefile | 63 | ||||
| -rw-r--r-- | biology/ugene/distinfo | 16 | ||||
| -rw-r--r-- | biology/ugene/files/patch-src-corelibs-U2Core-src-globals-AppResources.cpp | 73 | ||||
| -rw-r--r-- | biology/ugene/files/patch-src-shtirlitz-Shtirlitz.cpp | 14 | ||||
| -rw-r--r-- | biology/ugene/files/patch-src-ugenem-src-SendReportDialog.cpp | 49 | ||||
| -rw-r--r-- | biology/ugene/files/patch-src-ugeneui-src-Main.cpp | 20 | ||||
| -rw-r--r-- | biology/ugene/pkg-plist | 62 |
7 files changed, 71 insertions, 226 deletions
diff --git a/biology/ugene/Makefile b/biology/ugene/Makefile index 75778e5fc9ab..0bde5ed60d57 100644 --- a/biology/ugene/Makefile +++ b/biology/ugene/Makefile @@ -2,8 +2,8 @@ # $FreeBSD$ PORTNAME= ugene -DISTVERSION= 1.13.1 -CATEGORIES= biology +DISTVERSION= 1.14.0 +CATEGORIES= biology science MASTER_SITES= http://ugene.unipro.ru/downloads/ DISTFILES= ${DISTNAME}${EXTRACT_SUFX} QueryDesigner_UserManual.pdf \ UniproUGENE_UserManual.pdf WorkflowDesigner_UserManual.pdf @@ -17,7 +17,7 @@ LICENSE= GPLv2 RUN_DEPENDS= bash:${PORTSDIR}/shells/bash -USES= qmake execinfo +USES= execinfo qmake USE_GL= glu USE_QT4= gui webkit xml svg linguist_build moc_build qmake_build \ qtestlib_build rcc_build uic_build imageformats_run \ @@ -26,8 +26,8 @@ USE_XORG= xtst USE_LDCONFIG= yes INSTALLS_ICONS= yes -QMAKE_ARGS= INSTALL_PREFIX=${PREFIX} UGENE_INSTALL_DATA=${DATADIR} \ - INSTALL_MANDIR=${MAN1PREFIX}/man +QMAKE_ARGS= INSTALL_PREFIX="${PREFIX}" UGENE_INSTALL_DATA="${DATADIR}" \ + INSTALL_MANDIR="${MAN1PREFIX}/man" ALL_TARGET= release DOCSDIR= ${DATADIR}/manuals @@ -42,16 +42,19 @@ DOCS_DESC= Install official UGENE documentation (PDF) CXXFLAGS+= -std=c++11 .endif -.if ${ARCH} == "amd64" +.if ${ARCH} == amd64 # XXX: need to manually tell the build we are on x64 QMAKE_ARGS+= CONFIG+=x64 -PLIST_SUB= NOX64="@comment " +PLIST_SUB+= NOX64="@comment " .else -PLIST_SUB= NOX64="" +PLIST_SUB+= NOX64="" .endif .if ${MACHINE_CPU:Msse2} QMAKE_ARGS+= UGENE_SSE2_DETECTED=1 +PLIST_SUB+= SSE2="" +.else +PLIST_SUB+= SSE2="@comment " .endif post-extract: @@ -62,40 +65,14 @@ post-patch: @${REINPLACE_CMD} -e 's|/bin/bash|/usr/bin/env bash|' \ ${WRKSRC}/src/gen_bin_script.cmd \ ${WRKSRC}/installer/_common_data/ugene - @${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 &,' \ - ${WRKSRC}/src/ugenecl/Makefile.Release \ - ${WRKSRC}/src/ugeneui/Makefile.Release + @${REINPLACE_CMD} -e '/readproc\.h/d' \ + ${WRKSRC}/src/corelibs/U2Core/src/globals/AppResources.cpp + @${REINPLACE_CMD} -e '1000d' \ + ${WRKSRC}/src/plugins_3rdparty/ball/src/include/BALL/DATATYPE/string.h + @${REINPLACE_CMD} -e 's|-bit version|& for ${OPSYS}|' \ + ${WRKSRC}/src/ugeneui/src/main_window/AboutDialogController.cpp +.for x in ugenecl ugeneui plugins_checker + @${ECHO_CMD} 'LIBS += -lexecinfo' >> ${WRKSRC}/src/${x}/${x}.pro +.endfor .include <bsd.port.post.mk> diff --git a/biology/ugene/distinfo b/biology/ugene/distinfo index bbc6fb51abcc..dd384463de13 100644 --- a/biology/ugene/distinfo +++ b/biology/ugene/distinfo @@ -1,8 +1,8 @@ -SHA256 (ugene/ugene-1.13.1.tar.gz) = 00814743de631cc144e6f01955a5183bc668684de073f600e6491b504a7760c1 -SIZE (ugene/ugene-1.13.1.tar.gz) = 19098188 -SHA256 (ugene/QueryDesigner_UserManual.pdf) = 3c5bd735c02b7ac24bd319823fde2d175b750adc1c37fe7b17e2009452a00ddd -SIZE (ugene/QueryDesigner_UserManual.pdf) = 1306825 -SHA256 (ugene/UniproUGENE_UserManual.pdf) = 6c682c86f47a4c337eb4acdf0ae23ffa1b7fef1337d11e631655bfc943167b46 -SIZE (ugene/UniproUGENE_UserManual.pdf) = 12166178 -SHA256 (ugene/WorkflowDesigner_UserManual.pdf) = dd9a5e5860867a9a8f22d946dd94c34ee406aa648ff3d4220b0c2c5486e4bbeb -SIZE (ugene/WorkflowDesigner_UserManual.pdf) = 8963233 +SHA256 (ugene/ugene-1.14.0.tar.gz) = e54f67d54378fcb375029267bc1ae75aec5e6e4e7c9977184be5865475ef2c42 +SIZE (ugene/ugene-1.14.0.tar.gz) = 19777919 +SHA256 (ugene/QueryDesigner_UserManual.pdf) = 2add11809ecc3225abfef417ad8d5435fed76a662081f461abb36e3d4b31cfcd +SIZE (ugene/QueryDesigner_UserManual.pdf) = 824781 +SHA256 (ugene/UniproUGENE_UserManual.pdf) = c4aa20246988978c6b40a06f7753f78d204ee3155cb8876a3d665b9ebf5641db +SIZE (ugene/UniproUGENE_UserManual.pdf) = 12263913 +SHA256 (ugene/WorkflowDesigner_UserManual.pdf) = 9dc5b25bdc8d7af1473f5a860debebfd238bfef018cc7a9d69816354efcfa202 +SIZE (ugene/WorkflowDesigner_UserManual.pdf) = 8639016 diff --git a/biology/ugene/files/patch-src-corelibs-U2Core-src-globals-AppResources.cpp b/biology/ugene/files/patch-src-corelibs-U2Core-src-globals-AppResources.cpp deleted file mode 100644 index bfbfccd0be52..000000000000 --- a/biology/ugene/files/patch-src-corelibs-U2Core-src-globals-AppResources.cpp +++ /dev/null @@ -1,73 +0,0 @@ ---- 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_WIN - 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 - } - diff --git a/biology/ugene/files/patch-src-shtirlitz-Shtirlitz.cpp b/biology/ugene/files/patch-src-shtirlitz-Shtirlitz.cpp deleted file mode 100644 index 86be6655da16..000000000000 --- a/biology/ugene/files/patch-src-shtirlitz-Shtirlitz.cpp +++ /dev/null @@ -1,14 +0,0 @@ ---- 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 diff --git a/biology/ugene/files/patch-src-ugenem-src-SendReportDialog.cpp b/biology/ugene/files/patch-src-ugenem-src-SendReportDialog.cpp deleted file mode 100644 index 7f75a92202e3..000000000000 --- a/biology/ugene/files/patch-src-ugenem-src-SendReportDialog.cpp +++ /dev/null @@ -1,49 +0,0 @@ ---- 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 diff --git a/biology/ugene/files/patch-src-ugeneui-src-Main.cpp b/biology/ugene/files/patch-src-ugeneui-src-Main.cpp deleted file mode 100644 index cf7d556bfcf7..000000000000 --- a/biology/ugene/files/patch-src-ugeneui-src-Main.cpp +++ /dev/null @@ -1,20 +0,0 @@ ---- 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); - } diff --git a/biology/ugene/pkg-plist b/biology/ugene/pkg-plist index 9dc1c31b8314..f1822c8a7201 100644 --- a/biology/ugene/pkg-plist +++ b/biology/ugene/pkg-plist @@ -51,36 +51,20 @@ 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/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 -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 lib/ugene/plugins/ball.plugin lib/ugene/plugins/biostruct3d_view.license lib/ugene/plugins/biostruct3d_view.plugin +lib/ugene/plugins/browser_support.license +lib/ugene/plugins/browser_support.plugin lib/ugene/plugins/chroma_view.license lib/ugene/plugins/chroma_view.plugin lib/ugene/plugins/circular_view.license @@ -109,6 +93,8 @@ lib/ugene/plugins/gor4.license lib/ugene/plugins/gor4.plugin lib/ugene/plugins/hmm2.license lib/ugene/plugins/hmm2.plugin +%%SSE2%%lib/ugene/plugins/hmm3.license +%%SSE2%%lib/ugene/plugins/hmm3.plugin lib/ugene/plugins/kalign.license lib/ugene/plugins/kalign.plugin lib/ugene/plugins/libCoreTests.so @@ -135,6 +121,10 @@ 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/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/libchroma_view.so lib/ugene/plugins/libchroma_view.so.1 lib/ugene/plugins/libchroma_view.so.1.0 @@ -191,10 +181,18 @@ 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 +%%SSE2%%lib/ugene/plugins/libhmm3.so +%%SSE2%%lib/ugene/plugins/libhmm3.so.1 +%%SSE2%%lib/ugene/plugins/libhmm3.so.1.0 +%%SSE2%%lib/ugene/plugins/libhmm3.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/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/libopencl_support.so lib/ugene/plugins/libopencl_support.so.1 lib/ugene/plugins/libopencl_support.so.1.0 @@ -259,6 +257,10 @@ lib/ugene/plugins/libtest_runner.so.1.0.0 %%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/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/libweight_matrix.so lib/ugene/plugins/libweight_matrix.so.1 lib/ugene/plugins/libweight_matrix.so.1.0 @@ -267,6 +269,8 @@ 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/linkdata_support.license +lib/ugene/plugins/linkdata_support.plugin lib/ugene/plugins/opencl_support.license lib/ugene/plugins/opencl_support.plugin lib/ugene/plugins/orf_marker.license @@ -299,10 +303,13 @@ lib/ugene/plugins/test_runner.license lib/ugene/plugins/test_runner.plugin %%NOX64%%lib/ugene/plugins/umuscle.license %%NOX64%%lib/ugene/plugins/umuscle.plugin +lib/ugene/plugins/variants.license +lib/ugene/plugins/variants.plugin lib/ugene/plugins/weight_matrix.license lib/ugene/plugins/weight_matrix.plugin lib/ugene/plugins/workflow_designer.license lib/ugene/plugins/workflow_designer.plugin +lib/ugene/plugins_checker lib/ugene/transl_cs.qm lib/ugene/transl_en.qm lib/ugene/transl_ru.qm @@ -366,6 +373,7 @@ share/pixmaps/ugene.xpm %%DATADIR%%/cmdline/convert-seq.uwl %%DATADIR%%/cmdline/das_annotation.uwl %%DATADIR%%/cmdline/extract-sequence.uwl +%%DATADIR%%/cmdline/extract_consensus.uwl %%DATADIR%%/cmdline/fetch-sequence.uwl %%DATADIR%%/cmdline/find-orfs.uwl %%DATADIR%%/cmdline/find-repeats.uwl @@ -387,7 +395,16 @@ share/pixmaps/ugene.xpm %%DATADIR%%/cmdline/sitecon-build.uwl %%DATADIR%%/cmdline/sitecon-search.uwl %%DATADIR%%/cmdline/snp.uwl +%%DATADIR%%/custom_annotations/plasmid_features.txt %%DATADIR%%/enzymes/2013_08_01.bairoch.gz +%%DATADIR%%/genome_lengths/danRer7.genome +%%DATADIR%%/genome_lengths/ecoli.genome +%%DATADIR%%/genome_lengths/hg18.genome +%%DATADIR%%/genome_lengths/hg19.genome +%%DATADIR%%/genome_lengths/mm10.genome +%%DATADIR%%/genome_lengths/mm8.genome +%%DATADIR%%/genome_lengths/mm9.genome +%%DATADIR%%/genome_lengths/test.genome %%DATADIR%%/license %%PORTDOCS%%%%DOCSDIR%%/QueryDesigner_UserManual.pdf %%PORTDOCS%%%%DOCSDIR%%/UniproUGENE_UserManual.pdf @@ -1141,8 +1158,8 @@ 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/ACE/K26.ace %%DATADIR%%/samples/Assembly/chrM.fa %%DATADIR%%/samples/Assembly/chrM.sam %%DATADIR%%/samples/Assembly/chrM.sorted.bam @@ -1372,6 +1389,8 @@ 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/casava-fastq-filter.uwl +%%DATADIR%%/workflow_samples/Custom elements/fastq-trimmer.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 @@ -1395,12 +1414,15 @@ share/pixmaps/ugene.xpm %%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/extract_consensus.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/CASAVA FASTQ filter.usa %%DATADIR%%/workflow_samples/users/Dump sequence info.usa +%%DATADIR%%/workflow_samples/users/FASTQ Trimmer.usa %%DATADIR%%/workflow_samples/users/LinkData Fetch.usa %%DATADIR%%/workflow_samples/users/QualityFilter.usa @dirrm %%DATADIR%%/workflow_samples/users @@ -1456,7 +1478,9 @@ share/pixmaps/ugene.xpm @dirrm %%DATADIR%%/position_weight_matrix/JASPAR @dirrm %%DATADIR%%/position_weight_matrix %%PORTDOCS%%@dirrm %%DOCSDIR%% +@dirrm %%DATADIR%%/genome_lengths @dirrm %%DATADIR%%/enzymes +@dirrm %%DATADIR%%/custom_annotations @dirrm %%DATADIR%%/cmdline @dirrm %%DATADIR%%/biostruct3d_plugin @dirrm %%DATADIR%%/back_translation/Yeast |