Date: Mon, 11 Jun 2018 17:45:57 +0000 (UTC) From: Yuri Victorovich <yuri@FreeBSD.org> To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r472197 - head/biology/artemis Message-ID: <201806111745.w5BHjvpo090155@repo.freebsd.org>
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Author: yuri Date: Mon Jun 11 17:45:56 2018 New Revision: 472197 URL: https://svnweb.freebsd.org/changeset/ports/472197 Log: biology/artemis: Update 9 -> 17.0.1-11 Port changes: * Take maintainership * Change to github * Change to DISTVERSION * Add LICENSE * Depends on bash * Add USES=gmake * Remove NO_BUILD: needs to build jars from java files * Update the post-extract target * Change do-install to do minimal installation * Update WWW Modified: head/biology/artemis/Makefile head/biology/artemis/distinfo head/biology/artemis/pkg-descr head/biology/artemis/pkg-plist Modified: head/biology/artemis/Makefile ============================================================================== --- head/biology/artemis/Makefile Mon Jun 11 17:28:46 2018 (r472196) +++ head/biology/artemis/Makefile Mon Jun 11 17:45:56 2018 (r472197) @@ -2,34 +2,44 @@ # $FreeBSD$ PORTNAME= artemis -PORTVERSION= 9 -PORTREVISION= 2 +DISTVERSIONPREFIX= v +DISTVERSION= 17.0.1-11 +DISTVERSIONSUFFIX= -g3e43d27e CATEGORIES= biology java -MASTER_SITES= http://www.sanger.ac.uk/Software/Artemis/v${PORTVERSION}/ -DISTNAME= artemis_compiled_v${PORTVERSION} -MAINTAINER= ports@FreeBSD.org +MAINTAINER= yuri@FreeBSD.org COMMENT= DNA sequence viewer and annotation tool -WRKSRC= ${WRKDIR}/${PORTNAME} +LICENSE= GPLv3 +LICENSE_FILE= ${WRKSRC}/LICENSE -USES= shebangfix -SHEBANG_FILES= etc/go_associations.pl -perl_OLD_CMD= /usr/local/bin/perl5.6.1 +RUN_DEPENDS= bash:shells/bash + +USES= gmake shebangfix +USE_GITHUB= yes +GH_ACCOUNT= sanger-pathogens +SHEBANG_FILES= act art bamview dnaplotter test/*.sh etc/go_associations.pl USE_JAVA= yes JAVA_VERSION= 1.6+ +ALL_TARGET= jar NO_ARCH= yes -NO_BUILD= yes PLIST_SUB= PORTVERSION="${PORTVERSION}" post-extract: - @${FIND} ${WRKSRC} -type d -name CVS -exec ${RM} -r {} + + @cd ${WRKDIR} && ${MV} Artemis-${DISTVERSION}${DISTVERSIONSUFFIX} ${PORTNAME}-${DISTVERSION}${DISTVERSIONSUFFIX} do-install: @${MKDIR} ${STAGEDIR}${PREFIX}/${PORTNAME}-${PORTVERSION} - @${TAR} -C ${WRKSRC} -cf- . | ${TAR} -C ${STAGEDIR}${PREFIX}/${PORTNAME}-${PORTVERSION} -xpf- - @${LN} -s ../${PORTNAME}-${PORTVERSION}/art ${STAGEDIR}${PREFIX}/bin/art - @${LN} -s ../${PORTNAME}-${PORTVERSION}/act ${STAGEDIR}${PREFIX}/bin/act +.for f in jar_build lib etc images artemis_sqlmap + @cd ${WRKSRC} && ${COPYTREE_SHARE} ${f} ${STAGEDIR}${PREFIX}/${PORTNAME}-${PORTVERSION} +.endfor + @cd ${STAGEDIR}${PREFIX}/${PORTNAME}-${PORTVERSION} && ${MV} jar_build jars +.for f in art act bamview dnaplotter + ${INSTALL_SCRIPT} ${WRKSRC}/${f} ${STAGEDIR}${PREFIX}/${PORTNAME}-${PORTVERSION}/${f} + @${REINPLACE_CMD} -i '' -e 's|APPLICATION_HOME=.*|&/jars|' ${STAGEDIR}${PREFIX}/${PORTNAME}-${PORTVERSION}/${f} + @(${ECHO} "#!/bin/sh"; ${ECHO} ""; ${ECHO} "cd ${PREFIX}/${PORTNAME}-${PORTVERSION} && ./${f}") > ${STAGEDIR}${PREFIX}/bin/${f} + @${CHMOD} +x ${STAGEDIR}${PREFIX}/bin/${f} +.endfor .include <bsd.port.mk> Modified: head/biology/artemis/distinfo ============================================================================== --- head/biology/artemis/distinfo Mon Jun 11 17:28:46 2018 (r472196) +++ head/biology/artemis/distinfo Mon Jun 11 17:45:56 2018 (r472197) @@ -1,2 +1,3 @@ -SHA256 (artemis_compiled_v9.tar.gz) = ec61fdb7915322b5d6c8ac53aa3576cfe1a5042cc3c738e168306fdbaf4bcbe5 -SIZE (artemis_compiled_v9.tar.gz) = 6310269 +TIMESTAMP = 1528734532 +SHA256 (sanger-pathogens-artemis-v17.0.1-11-g3e43d27e_GH0.tar.gz) = a490d4b76bfdd8a531d22f2e0495e8c2c6e8efad18e6a9a0043ac425c7ab16dc +SIZE (sanger-pathogens-artemis-v17.0.1-11-g3e43d27e_GH0.tar.gz) = 77195529 Modified: head/biology/artemis/pkg-descr ============================================================================== --- head/biology/artemis/pkg-descr Mon Jun 11 17:28:46 2018 (r472196) +++ head/biology/artemis/pkg-descr Mon Jun 11 17:45:56 2018 (r472197) @@ -9,5 +9,4 @@ on Artemis. It can open two or more sequences (and the annotations/features) together with their comparisons (usually the result of running blastn or tblastx searches). -WWW: http://www.sanger.ac.uk/Software/Artemis/manual -WWW: http://www.sanger.ac.uk/Software/ACT/manual +WWW: https://www.sanger.ac.uk/science/tools/artemis Modified: head/biology/artemis/pkg-plist ============================================================================== --- head/biology/artemis/pkg-plist Mon Jun 11 17:28:46 2018 (r472196) +++ head/biology/artemis/pkg-plist Mon Jun 11 17:45:56 2018 (r472197) @@ -1,8 +1,8 @@ -artemis-%%PORTVERSION%%/README artemis-%%PORTVERSION%%/act artemis-%%PORTVERSION%%/art artemis-%%PORTVERSION%%/artemis_sqlmap/Analysis.xml artemis-%%PORTVERSION%%/artemis_sqlmap/AnalysisFeature.xml +artemis-%%PORTVERSION%%/artemis_sqlmap/Cv.xml artemis-%%PORTVERSION%%/artemis_sqlmap/CvTerm.xml artemis-%%PORTVERSION%%/artemis_sqlmap/Db.xml artemis-%%PORTVERSION%%/artemis_sqlmap/DbXRef.xml @@ -14,12 +14,19 @@ artemis-%%PORTVERSION%%/artemis_sqlmap/FeatureCvTermPu artemis-%%PORTVERSION%%/artemis_sqlmap/FeatureDbXRef.xml artemis-%%PORTVERSION%%/artemis_sqlmap/FeatureLoc.xml artemis-%%PORTVERSION%%/artemis_sqlmap/FeatureProp.xml +artemis-%%PORTVERSION%%/artemis_sqlmap/FeaturePub.xml artemis-%%PORTVERSION%%/artemis_sqlmap/FeatureRelationship.xml +artemis-%%PORTVERSION%%/artemis_sqlmap/FeatureSynonym.xml +artemis-%%PORTVERSION%%/artemis_sqlmap/Graph.xml artemis-%%PORTVERSION%%/artemis_sqlmap/Organism.xml +artemis-%%PORTVERSION%%/artemis_sqlmap/OrganismProp.xml artemis-%%PORTVERSION%%/artemis_sqlmap/Pub.xml +artemis-%%PORTVERSION%%/artemis_sqlmap/PubDbXRef.xml artemis-%%PORTVERSION%%/artemis_sqlmap/Synonym.xml artemis-%%PORTVERSION%%/artemis_sqlmap/chado_iBatis_config.properties artemis-%%PORTVERSION%%/artemis_sqlmap/chado_iBatis_config.xml +artemis-%%PORTVERSION%%/bamview +artemis-%%PORTVERSION%%/dnaplotter artemis-%%PORTVERSION%%/etc/af063097.embl artemis-%%PORTVERSION%%/etc/af063097.fasta artemis-%%PORTVERSION%%/etc/af063097_v_b132222.crunch @@ -30,45 +37,73 @@ artemis-%%PORTVERSION%%/etc/c1215.blastn.tab artemis-%%PORTVERSION%%/etc/c1215.embl artemis-%%PORTVERSION%%/etc/c1215.genbank artemis-%%PORTVERSION%%/etc/c1215.seq +artemis-%%PORTVERSION%%/etc/chado_extra.sql artemis-%%PORTVERSION%%/etc/feature_keys artemis-%%PORTVERSION%%/etc/feature_keys_gff artemis-%%PORTVERSION%%/etc/go_associations.pl +artemis-%%PORTVERSION%%/etc/key_mapping artemis-%%PORTVERSION%%/etc/log4j.properties +artemis-%%PORTVERSION%%/etc/log4j.properties.txt artemis-%%PORTVERSION%%/etc/options artemis-%%PORTVERSION%%/etc/pombe.usage +artemis-%%PORTVERSION%%/etc/project.properties +artemis-%%PORTVERSION%%/etc/qualifier_mapping artemis-%%PORTVERSION%%/etc/qualifier_types artemis-%%PORTVERSION%%/etc/qualifier_types_gff +artemis-%%PORTVERSION%%/etc/readmeDNADraw.html artemis-%%PORTVERSION%%/etc/results_to_netscape artemis-%%PORTVERSION%%/etc/run_blastn artemis-%%PORTVERSION%%/etc/run_blastn.sanger artemis-%%PORTVERSION%%/etc/run_blastp artemis-%%PORTVERSION%%/etc/run_blastp.sanger +artemis-%%PORTVERSION%%/etc/run_blastp.sanger.linux artemis-%%PORTVERSION%%/etc/run_blastx artemis-%%PORTVERSION%%/etc/run_blastx.sanger artemis-%%PORTVERSION%%/etc/run_clustalx artemis-%%PORTVERSION%%/etc/run_clustalx.sanger artemis-%%PORTVERSION%%/etc/run_fasta artemis-%%PORTVERSION%%/etc/run_fasta.sanger +artemis-%%PORTVERSION%%/etc/run_fasta.sanger.linux artemis-%%PORTVERSION%%/etc/run_fastx artemis-%%PORTVERSION%%/etc/run_fastx.sanger artemis-%%PORTVERSION%%/etc/run_hth artemis-%%PORTVERSION%%/etc/run_jalview +artemis-%%PORTVERSION%%/etc/run_netblastp artemis-%%PORTVERSION%%/etc/run_pepstats artemis-%%PORTVERSION%%/etc/run_sigcleave artemis-%%PORTVERSION%%/etc/run_smart artemis-%%PORTVERSION%%/etc/run_tblastn artemis-%%PORTVERSION%%/etc/run_tblastx +artemis-%%PORTVERSION%%/etc/run_tblastx.sanger +artemis-%%PORTVERSION%%/etc/versions +artemis-%%PORTVERSION%%/etc/writedb_entry +artemis-%%PORTVERSION%%/images/Wellcome_Sanger_Institute_Logo_Landscape_Digital_RGB_Full_Colour.jpg +artemis-%%PORTVERSION%%/images/act.gif artemis-%%PORTVERSION%%/images/helix.gif artemis-%%PORTVERSION%%/images/icon.gif artemis-%%PORTVERSION%%/images/sanger-centre.gif +artemis-%%PORTVERSION%%/jars/act.jar +artemis-%%PORTVERSION%%/jars/artemis.jar +artemis-%%PORTVERSION%%/jars/bamview.jar +artemis-%%PORTVERSION%%/jars/dnaplotter.jar artemis-%%PORTVERSION%%/lib/LICENSE.Apache artemis-%%PORTVERSION%%/lib/LICENSE.JDBC +artemis-%%PORTVERSION%%/lib/LICENSE.Picard artemis-%%PORTVERSION%%/lib/README +artemis-%%PORTVERSION%%/lib/batik/batik-awt-util.jar +artemis-%%PORTVERSION%%/lib/batik/batik-codec.jar +artemis-%%PORTVERSION%%/lib/batik/batik-dom.jar +artemis-%%PORTVERSION%%/lib/batik/batik-ext.jar +artemis-%%PORTVERSION%%/lib/batik/batik-svggen.jar +artemis-%%PORTVERSION%%/lib/batik/batik-util.jar +artemis-%%PORTVERSION%%/lib/batik/batik-xml.jar +artemis-%%PORTVERSION%%/lib/batik/version artemis-%%PORTVERSION%%/lib/biojava.jar -artemis-%%PORTVERSION%%/lib/chado-14-interface.jar +artemis-%%PORTVERSION%%/lib/commons-lang-2.6.jar +artemis-%%PORTVERSION%%/lib/commons-net-3.6.jar artemis-%%PORTVERSION%%/lib/ibatis/README -artemis-%%PORTVERSION%%/lib/ibatis/cglib-nodep-2.2_beta1.jar -artemis-%%PORTVERSION%%/lib/ibatis/ibatis-2.3.0.677.jar +artemis-%%PORTVERSION%%/lib/ibatis/cglib-nodep-2.2.jar +artemis-%%PORTVERSION%%/lib/ibatis/ibatis-2.3.4.726.jar artemis-%%PORTVERSION%%/lib/ibatis/license.txt artemis-%%PORTVERSION%%/lib/ibatis/log4j-1.2.14.jar artemis-%%PORTVERSION%%/lib/j2ssh/COMMONS.LICENSE @@ -80,1702 +115,10 @@ artemis-%%PORTVERSION%%/lib/j2ssh/j2ssh-core.jar artemis-%%PORTVERSION%%/lib/j2ssh/j2ssh.properties artemis-%%PORTVERSION%%/lib/jakarta-regexp-1.2.jar artemis-%%PORTVERSION%%/lib/jemAlign.jar -artemis-%%PORTVERSION%%/lib/jobcontrol.jar -artemis-%%PORTVERSION%%/lib/macos.jar -artemis-%%PORTVERSION%%/lib/postgresql-8.1-407.jdbc2ee.jar -artemis-%%PORTVERSION%%/lib/retrotranslator-runtime-1.1.0.jar -artemis-%%PORTVERSION%%/nsdb/CommitFailed.class -artemis-%%PORTVERSION%%/nsdb/CommitFailed.java -artemis-%%PORTVERSION%%/nsdb/CommitFailedHelper.class -artemis-%%PORTVERSION%%/nsdb/CommitFailedHelper.java -artemis-%%PORTVERSION%%/nsdb/CommitFailedHolder.java -artemis-%%PORTVERSION%%/nsdb/Datestamp.class -artemis-%%PORTVERSION%%/nsdb/Datestamp.java -artemis-%%PORTVERSION%%/nsdb/DatestampHelper.class -artemis-%%PORTVERSION%%/nsdb/DatestampHelper.java -artemis-%%PORTVERSION%%/nsdb/DatestampHolder.java -artemis-%%PORTVERSION%%/nsdb/Embl.class -artemis-%%PORTVERSION%%/nsdb/Embl.java -artemis-%%PORTVERSION%%/nsdb/EmblHelper.class -artemis-%%PORTVERSION%%/nsdb/EmblHelper.java -artemis-%%PORTVERSION%%/nsdb/EmblHolder.java -artemis-%%PORTVERSION%%/nsdb/EmblOperations.class -artemis-%%PORTVERSION%%/nsdb/EmblOperations.java -artemis-%%PORTVERSION%%/nsdb/EmblPackage/Superceded.class -artemis-%%PORTVERSION%%/nsdb/EmblPackage/Superceded.java -artemis-%%PORTVERSION%%/nsdb/EmblPackage/SupercededHelper.class -artemis-%%PORTVERSION%%/nsdb/EmblPackage/SupercededHelper.java -artemis-%%PORTVERSION%%/nsdb/EmblPackage/SupercededHolder.java -artemis-%%PORTVERSION%%/nsdb/EmblSeq.class -artemis-%%PORTVERSION%%/nsdb/EmblSeq.java -artemis-%%PORTVERSION%%/nsdb/EmblSeqHelper.class -artemis-%%PORTVERSION%%/nsdb/EmblSeqHelper.java -artemis-%%PORTVERSION%%/nsdb/EmblSeqHolder.java -artemis-%%PORTVERSION%%/nsdb/EmblSeqOperations.class -artemis-%%PORTVERSION%%/nsdb/EmblSeqOperations.java -artemis-%%PORTVERSION%%/nsdb/EmblSeqWriter.class -artemis-%%PORTVERSION%%/nsdb/EmblSeqWriter.java -artemis-%%PORTVERSION%%/nsdb/EmblSeqWriterHelper.class -artemis-%%PORTVERSION%%/nsdb/EmblSeqWriterHelper.java -artemis-%%PORTVERSION%%/nsdb/EmblSeqWriterHolder.java -artemis-%%PORTVERSION%%/nsdb/EmblSeqWriterOperations.class -artemis-%%PORTVERSION%%/nsdb/EmblSeqWriterOperations.java -artemis-%%PORTVERSION%%/nsdb/EmblWriter.class -artemis-%%PORTVERSION%%/nsdb/EmblWriter.java -artemis-%%PORTVERSION%%/nsdb/EmblWriterHelper.class -artemis-%%PORTVERSION%%/nsdb/EmblWriterHelper.java -artemis-%%PORTVERSION%%/nsdb/EmblWriterHolder.java -artemis-%%PORTVERSION%%/nsdb/EmblWriterOperations.class -artemis-%%PORTVERSION%%/nsdb/EmblWriterOperations.java -artemis-%%PORTVERSION%%/nsdb/EntryInfo.class -artemis-%%PORTVERSION%%/nsdb/EntryInfo.java -artemis-%%PORTVERSION%%/nsdb/EntryInfoHelper.java -artemis-%%PORTVERSION%%/nsdb/EntryInfoHolder.java -artemis-%%PORTVERSION%%/nsdb/EntryInfoListHelper.java -artemis-%%PORTVERSION%%/nsdb/EntryInfoListHolder.java -artemis-%%PORTVERSION%%/nsdb/EntryInfoOperations.class -artemis-%%PORTVERSION%%/nsdb/EntryInfoOperations.java -artemis-%%PORTVERSION%%/nsdb/EntryStats.class -artemis-%%PORTVERSION%%/nsdb/EntryStats.java -artemis-%%PORTVERSION%%/nsdb/EntryStatsHelper.class -artemis-%%PORTVERSION%%/nsdb/EntryStatsHelper.java -artemis-%%PORTVERSION%%/nsdb/EntryStatsHolder.java -artemis-%%PORTVERSION%%/nsdb/FeatureLocation.class -artemis-%%PORTVERSION%%/nsdb/FeatureLocation.java -artemis-%%PORTVERSION%%/nsdb/FeatureLocationHelper.class -artemis-%%PORTVERSION%%/nsdb/FeatureLocationHelper.java -artemis-%%PORTVERSION%%/nsdb/FeatureLocationHolder.java -artemis-%%PORTVERSION%%/nsdb/FeatureLocationListHelper.java -artemis-%%PORTVERSION%%/nsdb/FeatureLocationListHolder.java -artemis-%%PORTVERSION%%/nsdb/FeatureLocationOperations.class -artemis-%%PORTVERSION%%/nsdb/FeatureLocationOperations.java -artemis-%%PORTVERSION%%/nsdb/InexactLocation.class -artemis-%%PORTVERSION%%/nsdb/InexactLocation.java -artemis-%%PORTVERSION%%/nsdb/InexactLocationHelper.class -artemis-%%PORTVERSION%%/nsdb/InexactLocationHelper.java -artemis-%%PORTVERSION%%/nsdb/InexactLocationHolder.java -artemis-%%PORTVERSION%%/nsdb/InvalidKey.class -artemis-%%PORTVERSION%%/nsdb/InvalidKey.java -artemis-%%PORTVERSION%%/nsdb/InvalidKeyHelper.class -artemis-%%PORTVERSION%%/nsdb/InvalidKeyHelper.java -artemis-%%PORTVERSION%%/nsdb/InvalidKeyHolder.java -artemis-%%PORTVERSION%%/nsdb/InvalidQualifier.class -artemis-%%PORTVERSION%%/nsdb/InvalidQualifier.java -artemis-%%PORTVERSION%%/nsdb/InvalidQualifierHelper.class -artemis-%%PORTVERSION%%/nsdb/InvalidQualifierHelper.java -artemis-%%PORTVERSION%%/nsdb/InvalidQualifierHolder.java -artemis-%%PORTVERSION%%/nsdb/Location.class -artemis-%%PORTVERSION%%/nsdb/Location.java -artemis-%%PORTVERSION%%/nsdb/LocationHelper.class -artemis-%%PORTVERSION%%/nsdb/LocationHelper.java -artemis-%%PORTVERSION%%/nsdb/LocationHolder.java -artemis-%%PORTVERSION%%/nsdb/LocationListHelper.java -artemis-%%PORTVERSION%%/nsdb/LocationListHolder.java -artemis-%%PORTVERSION%%/nsdb/LocationOperations.class -artemis-%%PORTVERSION%%/nsdb/LocationOperations.java -artemis-%%PORTVERSION%%/nsdb/LocationPackage/IdListHelper.class -artemis-%%PORTVERSION%%/nsdb/LocationPackage/IdListHelper.java -artemis-%%PORTVERSION%%/nsdb/LocationPackage/IdListHolder.java -artemis-%%PORTVERSION%%/nsdb/LocationPackage/LocGapHelper.class -artemis-%%PORTVERSION%%/nsdb/LocationPackage/LocGapHelper.java -artemis-%%PORTVERSION%%/nsdb/LocationPackage/LocNodeTypeCodeHelper.class -artemis-%%PORTVERSION%%/nsdb/LocationPackage/LocNodeTypeCodeHelper.java -artemis-%%PORTVERSION%%/nsdb/LocationPackage/LocOperator.class -artemis-%%PORTVERSION%%/nsdb/LocationPackage/LocOperator.java -artemis-%%PORTVERSION%%/nsdb/LocationPackage/LocOperatorHelper.class -artemis-%%PORTVERSION%%/nsdb/LocationPackage/LocOperatorHelper.java -artemis-%%PORTVERSION%%/nsdb/LocationPackage/LocOperatorHolder.java -artemis-%%PORTVERSION%%/nsdb/LocationPackage/LocPhysicalSegmentHelper.class -artemis-%%PORTVERSION%%/nsdb/LocationPackage/LocPhysicalSegmentHelper.java -artemis-%%PORTVERSION%%/nsdb/LocationPackage/LocVirtualSegment.class -artemis-%%PORTVERSION%%/nsdb/LocationPackage/LocVirtualSegment.java -artemis-%%PORTVERSION%%/nsdb/LocationPackage/LocVirtualSegmentHelper.class -artemis-%%PORTVERSION%%/nsdb/LocationPackage/LocVirtualSegmentHelper.java -artemis-%%PORTVERSION%%/nsdb/LocationPackage/LocVirtualSegmentHolder.java -artemis-%%PORTVERSION%%/nsdb/LocationPackage/LocationNodeListHelper.class -artemis-%%PORTVERSION%%/nsdb/LocationPackage/LocationNodeListHelper.java -artemis-%%PORTVERSION%%/nsdb/LocationPackage/LocationNodeListHolder.java -artemis-%%PORTVERSION%%/nsdb/LocationPackage/LocationNode_u.class -artemis-%%PORTVERSION%%/nsdb/LocationPackage/LocationNode_u.java -artemis-%%PORTVERSION%%/nsdb/LocationPackage/LocationNode_uHelper.class -artemis-%%PORTVERSION%%/nsdb/LocationPackage/LocationNode_uHelper.java -artemis-%%PORTVERSION%%/nsdb/LocationPackage/LocationNode_uHolder.java -artemis-%%PORTVERSION%%/nsdb/LocationParse.class -artemis-%%PORTVERSION%%/nsdb/LocationParse.java -artemis-%%PORTVERSION%%/nsdb/LocationParseHelper.class -artemis-%%PORTVERSION%%/nsdb/LocationParseHelper.java -artemis-%%PORTVERSION%%/nsdb/LocationParseHolder.java -artemis-%%PORTVERSION%%/nsdb/NucFeature.class -artemis-%%PORTVERSION%%/nsdb/NucFeature.java -artemis-%%PORTVERSION%%/nsdb/NucFeatureHelper.class -artemis-%%PORTVERSION%%/nsdb/NucFeatureHelper.java -artemis-%%PORTVERSION%%/nsdb/NucFeatureHolder.java -artemis-%%PORTVERSION%%/nsdb/NucFeatureListHelper.class -artemis-%%PORTVERSION%%/nsdb/NucFeatureListHelper.java -artemis-%%PORTVERSION%%/nsdb/NucFeatureListHolder.java -artemis-%%PORTVERSION%%/nsdb/NucFeatureOperations.class -artemis-%%PORTVERSION%%/nsdb/NucFeatureOperations.java -artemis-%%PORTVERSION%%/nsdb/NucFeaturePackage/Qualifier.class -artemis-%%PORTVERSION%%/nsdb/NucFeaturePackage/Qualifier.java -artemis-%%PORTVERSION%%/nsdb/NucFeaturePackage/QualifierHelper.class -artemis-%%PORTVERSION%%/nsdb/NucFeaturePackage/QualifierHelper.java -artemis-%%PORTVERSION%%/nsdb/NucFeaturePackage/QualifierHolder.java -artemis-%%PORTVERSION%%/nsdb/NucFeaturePackage/QualifierListHelper.class -artemis-%%PORTVERSION%%/nsdb/NucFeaturePackage/QualifierListHelper.java -artemis-%%PORTVERSION%%/nsdb/NucFeaturePackage/QualifierListHolder.java -artemis-%%PORTVERSION%%/nsdb/NucFeaturePackage/QualifierTypeCodeHelper.class -artemis-%%PORTVERSION%%/nsdb/NucFeaturePackage/QualifierTypeCodeHelper.java -artemis-%%PORTVERSION%%/nsdb/NucFeaturePackage/QualifierValueListHelper.class -artemis-%%PORTVERSION%%/nsdb/NucFeaturePackage/QualifierValueListHelper.java -artemis-%%PORTVERSION%%/nsdb/NucFeaturePackage/QualifierValueListHolder.java -artemis-%%PORTVERSION%%/nsdb/NucFeaturePackage/QualifierValue_u.class -artemis-%%PORTVERSION%%/nsdb/NucFeaturePackage/QualifierValue_u.java -artemis-%%PORTVERSION%%/nsdb/NucFeaturePackage/QualifierValue_uHelper.class -artemis-%%PORTVERSION%%/nsdb/NucFeaturePackage/QualifierValue_uHelper.java -artemis-%%PORTVERSION%%/nsdb/NucFeaturePackage/QualifierValue_uHolder.java -artemis-%%PORTVERSION%%/nsdb/NucFeatureWriter.class -artemis-%%PORTVERSION%%/nsdb/NucFeatureWriter.java -artemis-%%PORTVERSION%%/nsdb/NucFeatureWriterHelper.class -artemis-%%PORTVERSION%%/nsdb/NucFeatureWriterHelper.java -artemis-%%PORTVERSION%%/nsdb/NucFeatureWriterHolder.java -artemis-%%PORTVERSION%%/nsdb/NucFeatureWriterListHelper.java -artemis-%%PORTVERSION%%/nsdb/NucFeatureWriterListHolder.java -artemis-%%PORTVERSION%%/nsdb/NucFeatureWriterOperations.class -artemis-%%PORTVERSION%%/nsdb/NucFeatureWriterOperations.java -artemis-%%PORTVERSION%%/nsdb/NucSeq.class -artemis-%%PORTVERSION%%/nsdb/NucSeq.java -artemis-%%PORTVERSION%%/nsdb/NucSeqHelper.java -artemis-%%PORTVERSION%%/nsdb/NucSeqHolder.java -artemis-%%PORTVERSION%%/nsdb/NucSeqListHelper.java -artemis-%%PORTVERSION%%/nsdb/NucSeqListHolder.java -artemis-%%PORTVERSION%%/nsdb/NucSeqOperations.class -artemis-%%PORTVERSION%%/nsdb/NucSeqOperations.java -artemis-%%PORTVERSION%%/nsdb/OutOfDate.class -artemis-%%PORTVERSION%%/nsdb/OutOfDate.java -artemis-%%PORTVERSION%%/nsdb/OutOfDateHelper.class -artemis-%%PORTVERSION%%/nsdb/OutOfDateHelper.java -artemis-%%PORTVERSION%%/nsdb/OutOfDateHolder.java -artemis-%%PORTVERSION%%/nsdb/QualifierParse.class -artemis-%%PORTVERSION%%/nsdb/QualifierParse.java -artemis-%%PORTVERSION%%/nsdb/QualifierParseHelper.class -artemis-%%PORTVERSION%%/nsdb/QualifierParseHelper.java -artemis-%%PORTVERSION%%/nsdb/QualifierParseHolder.java -artemis-%%PORTVERSION%%/nsdb/ReadOnlyException.class -artemis-%%PORTVERSION%%/nsdb/ReadOnlyException.java -artemis-%%PORTVERSION%%/nsdb/ReadOnlyExceptionHelper.class -artemis-%%PORTVERSION%%/nsdb/ReadOnlyExceptionHelper.java -artemis-%%PORTVERSION%%/nsdb/ReadOnlyExceptionHolder.java -artemis-%%PORTVERSION%%/nsdb/ServerInfo.class -artemis-%%PORTVERSION%%/nsdb/ServerInfo.java -artemis-%%PORTVERSION%%/nsdb/ServerInfoHelper.class -artemis-%%PORTVERSION%%/nsdb/ServerInfoHelper.java 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-artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/FeaturePlotGroup.java -artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/FeaturePopup$1.class -artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/FeaturePopup$10.class -artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/FeaturePopup$11.class -artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/FeaturePopup$12.class -artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/FeaturePopup$13.class *** DIFF OUTPUT TRUNCATED AT 1000 LINES ***
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