Date: Mon, 1 Sep 2014 07:39:00 +0000 (UTC) From: Alexey Dokuchaev <danfe@FreeBSD.org> To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r366842 - in head/biology/ugene: . files Message-ID: <201409010739.s817d0vU063874@svn.freebsd.org>
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Author: danfe Date: Mon Sep 1 07:38:59 2014 New Revision: 366842 URL: http://svnweb.freebsd.org/changeset/ports/366842 QAT: https://qat.redports.org/buildarchive/r366842/ Log: - Update Unipro UGENE and documentation to version 1.14.0 - Remove patches integrated upstream (it's nice to have direct contact) - Sort USES and pkg-plist, cleanup Makefile a bit while here Approved by: maintainer (implicit) Deleted: head/biology/ugene/files/ Modified: head/biology/ugene/Makefile head/biology/ugene/distinfo head/biology/ugene/pkg-plist Modified: head/biology/ugene/Makefile ============================================================================== --- head/biology/ugene/Makefile Mon Sep 1 07:31:53 2014 (r366841) +++ head/biology/ugene/Makefile Mon Sep 1 07:38:59 2014 (r366842) @@ -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 docume 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> Modified: head/biology/ugene/distinfo ============================================================================== --- head/biology/ugene/distinfo Mon Sep 1 07:31:53 2014 (r366841) +++ head/biology/ugene/distinfo Mon Sep 1 07:38:59 2014 (r366842) @@ -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 Modified: head/biology/ugene/pkg-plist ============================================================================== --- head/biology/ugene/pkg-plist Mon Sep 1 07:31:53 2014 (r366841) +++ head/biology/ugene/pkg-plist Mon Sep 1 07:38:59 2014 (r366842) @@ -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. %%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.s 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
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