Date: Sat, 23 Feb 2013 04:50:48 +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: r312798 - in head/biology: . ugene ugene/files Message-ID: <201302230450.r1N4omd8056294@svn.freebsd.org>
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Author: danfe Date: Sat Feb 23 04:50:48 2013 New Revision: 312798 URL: http://svnweb.freebsd.org/changeset/ports/312798 Log: Add Unipro UGENE, a free open-source crowss-platform bioinformatics software. PR: ports/173387 Submitted by: Hannes Hauswedell Added: head/biology/ugene/ head/biology/ugene/Makefile (contents, props changed) head/biology/ugene/distinfo (contents, props changed) head/biology/ugene/files/ head/biology/ugene/files/patch-src-corelibs-U2Private-src-CrashHandler.cpp (contents, props changed) head/biology/ugene/pkg-descr (contents, props changed) head/biology/ugene/pkg-plist (contents, props changed) Modified: head/biology/Makefile Modified: head/biology/Makefile ============================================================================== --- head/biology/Makefile Sat Feb 23 04:30:20 2013 (r312797) +++ head/biology/Makefile Sat Feb 23 04:50:48 2013 (r312798) @@ -94,6 +94,7 @@ SUBDIR += tinker SUBDIR += treepuzzle SUBDIR += treeviewx + SUBDIR += ugene SUBDIR += velvet SUBDIR += wise SUBDIR += xdrawchem Added: head/biology/ugene/Makefile ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/ugene/Makefile Sat Feb 23 04:50:48 2013 (r312798) @@ -0,0 +1,48 @@ +# Created by: Hannes Hauswedell <h2+fbsdports@fsfe.org> +# $FreeBSD$ + +PORTNAME= ugene +DISTVERSION= 1.11.4 +CATEGORIES= biology +MASTER_SITES= http://ugene.unipro.ru/downloads/ + +MAINTAINER= h2+fbsdports@fsfe.org +COMMENT= Free, open-source, cross-platform bioinformatics toolkit + +LICENSE= GPLv2 + +LIB_DEPENDS= execinfo:${PORTSDIR}/devel/libexecinfo +RUN_DEPENDS= bash:${PORTSDIR}/shells/bash + +USE_GL= glu +USE_QT4= gui webkit xml svg linguist_build moc_build qmake_build \ + qtestlib_build rcc_build uic_build imageformats_run +USE_XORG= xtst + +USE_LDCONFIG= yes +INSTALLS_ICONS= yes +MAKE_JOBS_SAFE= yes + +MAN1= ${PORTNAME}.1 +MANCOMPRESSED= yes + +.include <bsd.port.pre.mk> + +.if ${ARCH} == "amd64" +# need to manually tell the build we are on x64 +CARCH= CONFIG+=x64 +.endif + +# yes, bash is required, stuff will not execute with sh +post-patch: + @${REINPLACE_CMD} -e 's|/bin/bash|/usr/bin/env bash|' \ + ${WRKSRC}/src/gen_bin_script.cmd \ + ${WRKSRC}/installer/_common_data/ugene + +do-configure: + @cd ${CONFIGURE_WRKSRC} && ${SETENV} ${CONFIGURE_ENV} ${QMAKE} \ + PREFIX=${PREFIX} INSTALL_PREFIX=${PREFIX} \ + INSTALL_MANDIR=${MAN1PREFIX}/man ${CARCH} \ + UGENE_INSTALL_DATA=${DATADIR} -r ${PORTNAME}.pro + +.include <bsd.port.post.mk> Added: head/biology/ugene/distinfo ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/ugene/distinfo Sat Feb 23 04:50:48 2013 (r312798) @@ -0,0 +1,2 @@ +SHA256 (ugene-1.11.4.tar.gz) = 5b9b914e7ef5a3d3658f3346cccdb5cd6583b03db3b7bed7e163cb5cfd5663fa +SIZE (ugene-1.11.4.tar.gz) = 14761290 Added: head/biology/ugene/files/patch-src-corelibs-U2Private-src-CrashHandler.cpp ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/ugene/files/patch-src-corelibs-U2Private-src-CrashHandler.cpp Sat Feb 23 04:50:48 2013 (r312798) @@ -0,0 +1,20 @@ +--- ./src/corelibs/U2Private/src/CrashHandler.cpp.old 2012-10-30 15:36:22.000000000 +0100 ++++ ./src/corelibs/U2Private/src/CrashHandler.cpp 2012-10-30 15:47:47.000000000 +0100 +@@ -253,7 +253,7 @@ + } + //handler = AddVectoredExceptionHandler(1, CrashHandlerFunc); + +-#elif defined( Q_OS_MAC) ++#elif defined( Q_OS_MAC ) || defined ( Q_OS_FREEBSD ) + return; //TODO: implement crash hander for MAC OS + #else + stack_t sigstk; +@@ -284,7 +284,7 @@ + void CrashHandler::runMonitorProcess(const QString &exceptionType) { + QString path = QCoreApplication::applicationDirPath() + "/ugenem"; + +-#ifndef Q_OS_WIN ++#if !defined ( Q_OS_WIN ) && !defined ( Q_OS_FREEBSD ) + char pid_buf[30]; + sprintf(pid_buf, "%d", getpid()); + char name_buf[512]; Added: head/biology/ugene/pkg-descr ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/ugene/pkg-descr Sat Feb 23 04:50:48 2013 (r312798) @@ -0,0 +1,12 @@ +Unipro UGENE is a multiplatform open-source software with the main goal of +assisting molecular biologists without much expertise in bioinformatics to +manage, analyze and visualize their data. UGENE integrates widely used +bioinformatics tools within a common user interface. + +The 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. + +WWW: http://ugene.unipro.ru/ Added: head/biology/ugene/pkg-plist ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/ugene/pkg-plist Sat Feb 23 04:50:48 2013 (r312798) @@ -0,0 +1,1135 @@ +bin/ugene +lib/ugene/libU2Algorithm.so +lib/ugene/libU2Core.so +lib/ugene/libU2Designer.so +lib/ugene/libU2Formats.so +lib/ugene/libU2Gui.so +lib/ugene/libU2Lang.so +lib/ugene/libU2Private.so +lib/ugene/libU2Remote.so +lib/ugene/libU2Test.so +lib/ugene/libU2View.so +lib/ugene/libgtest.so +lib/ugene/libugenedb.so +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/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/chroma_view.license +lib/ugene/plugins/chroma_view.plugin +lib/ugene/plugins/circular_view.license +lib/ugene/plugins/circular_view.plugin +lib/ugene/plugins/dbi_bam.license +lib/ugene/plugins/dbi_bam.plugin +lib/ugene/plugins/dna_export.license +lib/ugene/plugins/dna_export.plugin +lib/ugene/plugins/dna_flexibility.license +lib/ugene/plugins/dna_flexibility.plugin +lib/ugene/plugins/dna_graphpack.license +lib/ugene/plugins/dna_graphpack.plugin +lib/ugene/plugins/dna_stat.license +lib/ugene/plugins/dna_stat.plugin +lib/ugene/plugins/dotplot.license +lib/ugene/plugins/dotplot.plugin +lib/ugene/plugins/enzymes.license +lib/ugene/plugins/enzymes.plugin +lib/ugene/plugins/expert_discovery.license +lib/ugene/plugins/expert_discovery.plugin +lib/ugene/plugins/external_tool_support.license +lib/ugene/plugins/external_tool_support.plugin +lib/ugene/plugins/genome_aligner.license +lib/ugene/plugins/genome_aligner.plugin +lib/ugene/plugins/gor4.license +lib/ugene/plugins/gor4.plugin +lib/ugene/plugins/hmm2.license +lib/ugene/plugins/hmm2.plugin +lib/ugene/plugins/kalign.license +lib/ugene/plugins/kalign.plugin +lib/ugene/plugins/libCoreTests.so +lib/ugene/plugins/libGUITestBase.so +lib/ugene/plugins/libannotator.so +lib/ugene/plugins/libapi_tests.so +lib/ugene/plugins/libball.so +lib/ugene/plugins/libbiostruct3d_view.so +lib/ugene/plugins/libchroma_view.so +lib/ugene/plugins/libcircular_view.so +lib/ugene/plugins/libdbi_bam.so +lib/ugene/plugins/libdna_export.so +lib/ugene/plugins/libdna_flexibility.so +lib/ugene/plugins/libdna_graphpack.so +lib/ugene/plugins/libdna_stat.so +lib/ugene/plugins/libdotplot.so +lib/ugene/plugins/libenzymes.so +lib/ugene/plugins/libexpert_discovery.so +lib/ugene/plugins/libexternal_tool_support.so +lib/ugene/plugins/libgenome_aligner.so +lib/ugene/plugins/libgor4.so +lib/ugene/plugins/libhmm2.so +lib/ugene/plugins/libkalign.so +lib/ugene/plugins/libopencl_support.so +lib/ugene/plugins/liborf_marker.so +lib/ugene/plugins/libperf_monitor.so +lib/ugene/plugins/libphylip.so +lib/ugene/plugins/libprimer3.so +lib/ugene/plugins/libpsipred.so +lib/ugene/plugins/libptools.so +lib/ugene/plugins/libquery_designer.so +lib/ugene/plugins/libremote_blast.so +lib/ugene/plugins/libremote_service.so +lib/ugene/plugins/librepeat_finder.so +lib/ugene/plugins/libsitecon.so +lib/ugene/plugins/libsmith_waterman.so +lib/ugene/plugins/libtest_runner.so +lib/ugene/plugins/libweight_matrix.so +lib/ugene/plugins/libworkflow_designer.so +lib/ugene/plugins/opencl_support.license +lib/ugene/plugins/opencl_support.plugin +lib/ugene/plugins/orf_marker.license +lib/ugene/plugins/orf_marker.plugin +lib/ugene/plugins/perf_monitor.license +lib/ugene/plugins/perf_monitor.plugin +lib/ugene/plugins/phylip.license +lib/ugene/plugins/phylip.plugin +lib/ugene/plugins/primer3.license +lib/ugene/plugins/primer3.plugin +lib/ugene/plugins/psipred.license +lib/ugene/plugins/psipred.plugin +lib/ugene/plugins/ptools.license +lib/ugene/plugins/ptools.plugin +lib/ugene/plugins/query_designer.license +lib/ugene/plugins/query_designer.plugin +lib/ugene/plugins/remote_blast.license +lib/ugene/plugins/remote_blast.plugin +lib/ugene/plugins/remote_service.license +lib/ugene/plugins/remote_service.plugin +lib/ugene/plugins/repeat_finder.license +lib/ugene/plugins/repeat_finder.plugin +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/test_runner.license +lib/ugene/plugins/test_runner.plugin +lib/ugene/plugins/weight_matrix.license +lib/ugene/plugins/weight_matrix.plugin 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+%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Rpn4.pwm +%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Rsc3.pwm +%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Rsc30.pwm +%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Rtg3.pwm +%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Sfl1.pwm +%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Sfp1.pwm +%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Sip4.pwm +%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Skn7.pwm +%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Smp1.pwm +%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Spt15.pwm +%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Srd1.pwm +%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Stb3.pwm +%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Stp2.pwm +%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Stp4.pwm +%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Sum1.pwm +%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Sut2.pwm +%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Tbf1.pwm +%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Tbs1.pwm +%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Tea1.pwm +%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Tec1.pwm +%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Tye7.pwm +%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Ume6.pwm +%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Usv1.pwm +%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Xbp1.pwm +%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Yap1.pwm +%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Yap6.pwm +%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Ybr239c.pwm +%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Ydr520c.pwm +%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Yer130c.pwm +%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Ygr067c.pwm +%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Ykl222c.pwm +%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Yll054c.pwm +%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Yml081w.pwm +%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Ynr063w.pwm +%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Yox1.pwm +%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Ypr013c.pwm +%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Ypr015c.pwm +%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Ypr196w.pwm +%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Yrm1.pwm +%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Yrr1.pwm +%%DATADIR%%/position_weight_matrix/UniPROBE/NBT06/Cbf1.pwm +%%DATADIR%%/position_weight_matrix/UniPROBE/NBT06/Ceh-22.pwm +%%DATADIR%%/position_weight_matrix/UniPROBE/NBT06/Oct-1.pwm +%%DATADIR%%/position_weight_matrix/UniPROBE/NBT06/Rap1.pwm +%%DATADIR%%/position_weight_matrix/UniPROBE/NBT06/Zif268.pwm +%%DATADIR%%/position_weight_matrix/UniPROBE/PNAS08/Cgd2_3490.pwm +%%DATADIR%%/position_weight_matrix/UniPROBE/PNAS08/PF14_0633.pwm +%%DATADIR%%/position_weight_matrix/UniPROBE/PNAS08/PFF0200c.pwm 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+%%DATADIR%%/samples/Genbank/NC_014267.1.gb +%%DATADIR%%/samples/Genbank/PBR322.gb +%%DATADIR%%/samples/Genbank/murine.gb +%%DATADIR%%/samples/Genbank/sars.gb +%%DATADIR%%/samples/HMM/aligment15900.hmm +%%DATADIR%%/samples/MMDB/1CRN.prt +%%DATADIR%%/samples/MMDB/2JQS.prt +%%DATADIR%%/samples/MSF/HMA.msf +%%DATADIR%%/samples/MSF/lipid8.msf +%%DATADIR%%/samples/MSF/pla2_20.msf +%%DATADIR%%/samples/Newick/COI.nwk +%%DATADIR%%/samples/PDB/1CF7.PDB +%%DATADIR%%/samples/PDB/1CRN.PDB +%%DATADIR%%/samples/PDB/3INS.PDB +%%DATADIR%%/samples/Raw/raw.seq +%%DATADIR%%/samples/SCF/90-JRI-07.scf +%%DATADIR%%/samples/Stockholm/CBS.sto +%%DATADIR%%/samples/Stockholm/UPSK.sto +%%DATADIR%%/samples/Swiss-Prot/D0VTW9.txt +%%DATADIR%%/samples/Swiss-Prot/P01375.txt +%%DATADIR%%/samples/Swiss-Prot/P16152.txt +%%DATADIR%%/sitecon_models/eukaryotic/CEBP_a.sitecon.gz +%%DATADIR%%/sitecon_models/eukaryotic/CEBPall.sitecon.gz +%%DATADIR%%/sitecon_models/eukaryotic/CLOCK.sitecon.gz +%%DATADIR%%/sitecon_models/eukaryotic/CRE.sitecon.gz +%%DATADIR%%/sitecon_models/eukaryotic/E2F1.sitecon.gz +%%DATADIR%%/sitecon_models/eukaryotic/E2F1DP1sel1.sitecon.gz +%%DATADIR%%/sitecon_models/eukaryotic/EGR1.sitecon.gz +%%DATADIR%%/sitecon_models/eukaryotic/Eklf.sitecon.gz +%%DATADIR%%/sitecon_models/eukaryotic/GATA1.sitecon.gz +%%DATADIR%%/sitecon_models/eukaryotic/GATA_ALL.sitecon.gz +%%DATADIR%%/sitecon_models/eukaryotic/Gata2.sitecon.gz +%%DATADIR%%/sitecon_models/eukaryotic/Gata3.sitecon.gz +%%DATADIR%%/sitecon_models/eukaryotic/HMG1.sitecon.gz +%%DATADIR%%/sitecon_models/eukaryotic/HNF1.sitecon.gz +%%DATADIR%%/sitecon_models/eukaryotic/HNF3_4.sitecon.gz +%%DATADIR%%/sitecon_models/eukaryotic/HNF4.sitecon.gz +%%DATADIR%%/sitecon_models/eukaryotic/MYOGsel3.sitecon.gz +%%DATADIR%%/sitecon_models/eukaryotic/MyoD.sitecon.gz +%%DATADIR%%/sitecon_models/eukaryotic/NF1.sitecon.gz +%%DATADIR%%/sitecon_models/eukaryotic/NFATp.sitecon.gz +%%DATADIR%%/sitecon_models/eukaryotic/NFkB_all.sitecon.gz +%%DATADIR%%/sitecon_models/eukaryotic/NFkB_hetero.sitecon.gz +%%DATADIR%%/sitecon_models/eukaryotic/NFkB_homo.sitecon.gz +%%DATADIR%%/sitecon_models/eukaryotic/Nf_e2.sitecon.gz *** DIFF OUTPUT TRUNCATED AT 1000 LINES ***
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