- biology/act is redundant after biology/artemis update

PR:             ports/76217
Submitted by:   Fernan Aguero <fernan@iib.unsam.edu.ar>
Approved by:	maintainer timeout (2 monthes)

5 files changed, 0 insertions, 1648 deletions

diff --git a/biology/Makefile b/biology/Makefile
index 252e79a989e2..9e958371bc9f 100644
--- a/biology/Makefile
+++ b/biology/Makefile
@@ -4,7 +4,6 @@
     COMMENT = Biology
 
     SUBDIR += L-Breeder
-    SUBDIR += act
     SUBDIR += ariadne
     SUBDIR += artemis
     SUBDIR += avida
diff --git a/biology/act/Makefile b/biology/act/Makefile
deleted file mode 100644
index 5703175823f8..000000000000
--- a/biology/act/Makefile
+++ /dev/null
@@ -1,35 +0,0 @@
-# New ports collection makefile for:	artemis
-# Date created:		10 Mar 2003
-# Whom:			fernan@iib.unsam.edu.ar
-#
-# $FreeBSD$
-#
-
-PORTNAME=	act
-PORTVERSION=	2.0
-PORTREVISION=	1
-CATEGORIES=	biology
-MASTER_SITES=	http://www.sanger.ac.uk/Software/ACT/v2/
-DISTNAME=	act_compiled_v2
-
-MAINTAINER=	chuynh@biolateral.com.au
-COMMENT=	A DNA sequence comparison viewer based on Artemis
-
-RUN_DEPENDS=	${JAVA_COMMAND}:${PORTSDIR}/java/jdk13
-
-WRKSRC=		${WRKDIR}/${PORTNAME}
-
-JDK_VERSION=	1.3.1
-JDK_DIR=	${PREFIX}/jdk${JDK_VERSION}
-JAVA_COMMAND=	${JDK_DIR}/bin/java
-
-NO_BUILD=	yes
-
-do-install:
-	@${MKDIR} ${PREFIX}/${PORTNAME}-${PORTVERSION}
-	@${TAR} -C ${WRKSRC} -cf- . | ${TAR} -C ${PREFIX}/${PORTNAME}-${PORTVERSION} -xpf-
-	@${LN} -s ${PREFIX}/${PORTNAME}-${PORTVERSION}/act ${PREFIX}/bin/act
-
-PLIST_SUB=	PORTVERSION="${PORTVERSION}"
-
-.include <bsd.port.mk>
diff --git a/biology/act/distinfo b/biology/act/distinfo
deleted file mode 100644
index 673dc041aa3d..000000000000
--- a/biology/act/distinfo
+++ /dev/null
@@ -1,2 +0,0 @@
-MD5 (act_compiled_v2.tar.gz) = 7029fb9ac1beb63679a41cfea788e4f5
-SIZE (act_compiled_v2.tar.gz) = 4857410
diff --git a/biology/act/pkg-descr b/biology/act/pkg-descr
deleted file mode 100644
index f610f9519091..000000000000
--- a/biology/act/pkg-descr
+++ /dev/null
@@ -1,12 +0,0 @@
-ACT (Artemis Comparison Tool) is a DNA sequence comparison viewer based on
-Artemis. In common with Artemis, ACT is written in Java and runs on UNIX,
-GNU/Linux, Macintosh and MS Windows systems. It can read complete EMBL
-and GENBANK entries or sequence in FASTA or raw format. Extra sequence
-features can be in EMBL, GENBANK or GFF format. ACT is distributed under the
-same license as Artemis. 
-
-The sequence comparison displayed by ACT is usually the result of a blastn or
-tblastx search that has been processed by MSPcrunch. MSPcrunch must be run
-with the -d flag for the output to be usable by ACT. 
-
-WWW:  http://www.sanger.ac.uk/Software/ACT/manual
diff --git a/biology/act/pkg-plist b/biology/act/pkg-plist
deleted file mode 100644
index bfa40bc00500..000000000000
--- a/biology/act/pkg-plist
+++ /dev/null
@@ -1,1598 +0,0 @@
-act-2.0/CVS/Root
-act-2.0/CVS/Repository
-act-2.0/CVS/Entries
-act-2.0/.cvsignore
-act-2.0/AppGlobal.java
-act-2.0/Dad.java
-act-2.0/Makefile
-act-2.0/act
-act-2.0/icon.gif
-act-2.0/META-INF/CVS/Root
-act-2.0/META-INF/CVS/Repository
-act-2.0/META-INF/CVS/Entries
-act-2.0/META-INF/MANIFEST.MF
-act-2.0/diana/CVS/Root
-act-2.0/diana/CVS/Repository
-act-2.0/diana/CVS/Entries
-act-2.0/diana/Action.java
-act-2.0/diana/ActionController.java
-act-2.0/diana/ActionVector.java
-act-2.0/diana/AlignMatch.java
-act-2.0/diana/AlignMatchVector.java
-act-2.0/diana/AlignmentSelectionChangeEvent.java
-act-2.0/diana/AlignmentSelectionChangeListener.java
-act-2.0/diana/BlastM8ComparisonData.java
-act-2.0/diana/ChangeEvent.java
-act-2.0/diana/ChangeEventVector.java
-act-2.0/diana/ChangeListener.java
-act-2.0/diana/ClipBoard.java
-act-2.0/diana/ComparisonData.java
-act-2.0/diana/ComparisonDataFactory.java
-act-2.0/diana/Entry.java
-act-2.0/diana/plot/CVS/Root
-act-2.0/diana/plot/CVS/Repository
-act-2.0/diana/plot/CVS/Entries
-act-2.0/diana/plot/AGWindowAlgorithm.java
-act-2.0/diana/plot/ATDeviationAlgorithm.java
-act-2.0/diana/plot/Algorithm.java
-act-2.0/diana/plot/BaseAlgorithm.java
-act-2.0/diana/plot/Codon12CorrelationAlgorithm.java
-act-2.0/diana/plot/CodonUsageAlgorithm.java
-act-2.0/diana/plot/CodonUsageFormatException.java
-act-2.0/diana/plot/CodonUsageWeight.java
-act-2.0/diana/plot/CodonWeight.java
-act-2.0/diana/plot/CoilFeatureAlgorithm.java
-act-2.0/diana/plot/HydroAlgorithm.java
-act-2.0/diana/plot/FeatureAlgorithm.java
-act-2.0/diana/plot/GCDeviationAlgorithm.java
-act-2.0/diana/plot/GCFrameAlgorithm.java
-act-2.0/diana/plot/GCSDWindowAlgorithm.java
-act-2.0/diana/plot/GCWindowAlgorithm.java
-act-2.0/diana/plot/HydrophilicityAlgorithm.java
-act-2.0/diana/plot/HydrophobicityAlgorithm.java
-act-2.0/diana/plot/KarlinSigAlgorithm.java
-act-2.0/diana/plot/UserDataAlgorithm.java
-act-2.0/diana/plot/Algorithm.class
-act-2.0/diana/plot/BaseAlgorithm.class
-act-2.0/diana/plot/CodonUsageAlgorithm.class
-act-2.0/diana/plot/CodonWeight.class
-act-2.0/diana/plot/CodonUsageWeight.class
-act-2.0/diana/plot/Codon12CorrelationAlgorithm.class
-act-2.0/diana/plot/GCWindowAlgorithm.class
-act-2.0/diana/plot/GCSDWindowAlgorithm.class
-act-2.0/diana/plot/AGWindowAlgorithm.class
-act-2.0/diana/plot/GCFrameAlgorithm.class
-act-2.0/diana/plot/GCDeviationAlgorithm.class
-act-2.0/diana/plot/ATDeviationAlgorithm.class
-act-2.0/diana/plot/KarlinSigAlgorithm.class
-act-2.0/diana/plot/CodonUsageFormatException.class
-act-2.0/diana/plot/UserDataAlgorithm.class
-act-2.0/diana/plot/FeatureAlgorithm.class
-act-2.0/diana/plot/HydroAlgorithm.class
-act-2.0/diana/plot/HydrophobicityAlgorithm.class
-act-2.0/diana/plot/HydrophilicityAlgorithm.class
-act-2.0/diana/plot/CoilFeatureAlgorithm.class
-act-2.0/diana/ComparisonDataParseException.java
-act-2.0/diana/EntryChangeEvent.java
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-act-2.0/diana/EntryGroup.java
-act-2.0/diana/EntryGroupChangeEvent.java
-act-2.0/diana/EntryGroupChangeListener.java
-act-2.0/diana/EntrySource.java
-act-2.0/diana/EntrySourceVector.java
-act-2.0/diana/EntryVector.java
-act-2.0/diana/ExternalApplication.java
-act-2.0/diana/ExternalProgram.java
-act-2.0/diana/ExternalProgramException.java
-act-2.0/diana/ExternalProgramVector.java
-act-2.0/diana/ExternalSearchProgram.java
-act-2.0/diana/Feature.java
-act-2.0/diana/FeatureChangeEvent.java
-act-2.0/diana/FeatureChangeListener.java
-act-2.0/diana/FeatureEnumeration.java
-act-2.0/diana/FeatureFromVectorPredicate.java
-act-2.0/diana/FeatureKeyPredicate.java
-act-2.0/diana/FeaturePredicate.java
-act-2.0/diana/FeatureKeyQualifierPredicate.java
-act-2.0/diana/FeaturePatternPredicate.java
-act-2.0/diana/FeaturePredicateConjunction.java
-act-2.0/diana/FeatureSegment.java
-act-2.0/diana/FeatureSegmentVector.java
-act-2.0/diana/FeatureVector.java
-act-2.0/diana/FilteredEntryGroup.java
-act-2.0/diana/GotoEvent.java
-act-2.0/diana/GotoListener.java
-act-2.0/diana/GotoEventSource.java
-act-2.0/diana/LastSegmentException.java
-act-2.0/diana/Logger.java
-act-2.0/diana/MSPcrunchComparisonData.java
-act-2.0/diana/MUMmerComparisonData.java
-act-2.0/diana/MegaBlastComparisonData.java
-act-2.0/diana/OptionChangeEvent.java
-act-2.0/diana/OptionChangeListener.java
-act-2.0/diana/Options.java
-act-2.0/diana/SSAHAComparisonData.java
-act-2.0/diana/Selectable.java
-act-2.0/diana/Selection.java
-act-2.0/diana/SelectionChangeEvent.java
-act-2.0/diana/SelectionChangeListener.java
-act-2.0/diana/SimpleComparisonData.java
-act-2.0/diana/helix.gif
-act-2.0/diana/SimpleEntryGroup.java
-act-2.0/diana/SimpleGotoEventSource.java
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-act-2.0/diana/components/AddMenu.java
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-act-2.0/diana/components/AlignmentViewer.java
-act-2.0/diana/components/ArtemisCheckboxMenuItem.java
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-act-2.0/diana/components/BioJavaEntrySource.java
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-act-2.0/diana/components/ComparatorGlue.java
-act-2.0/diana/components/CorbaEntrySource.java
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-act-2.0/diana/components/DisplayComponent.java
-act-2.0/diana/components/EMBLCorbaEntrySource.java
-act-2.0/diana/components/EditMenu.java
-act-2.0/diana/components/EnsemblEntrySource.java
-act-2.0/diana/components/EntryActionListener.java
-act-2.0/diana/components/EntryEdit.java
-act-2.0/diana/components/EntryGroupMenu.java
-act-2.0/diana/components/EntryEditVector.java
-act-2.0/diana/components/EntryFileDialog.java
-act-2.0/diana/components/EntryGroupDisplay.java
-act-2.0/diana/components/EntryGroupInfoDisplay.java
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-act-2.0/diana/components/EntryHeaderEdit.java
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-act-2.0/type/CodonTranslationListHolder.java
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-act-2.0/type/Fuzzy.java
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-act-2.0/type/Greater_ftc.java
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-act-2.0/nsdb/FeatureLocationHolder.java
-act-2.0/nsdb/_FeatureLocationStub.java
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-act-2.0/nsdb/NucFeature.java
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-act-2.0/nsdb/NucFeatureHolder.java
-act-2.0/nsdb/_NucFeatureStub.java
-act-2.0/nsdb/NucFeaturePOATie.java
-act-2.0/nsdb/NucFeaturePackage/QualifierTypeCodeHelper.java
-act-2.0/nsdb/NucFeaturePackage/QualifierValue_u.java
-act-2.0/nsdb/NucFeaturePackage/QualifierValue_uHolder.java
-act-2.0/nsdb/NucFeaturePackage/QualifierValue_uHelper.java
-act-2.0/nsdb/NucFeaturePackage/QualifierValueListHolder.java
-act-2.0/nsdb/NucFeaturePackage/QualifierValueListHelper.java
-act-2.0/nsdb/NucFeaturePackage/Qualifier.java
-act-2.0/nsdb/NucFeaturePackage/QualifierHolder.java
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-act-2.0/nsdb/NucFeaturePackage/QualifierListHolder.java
-act-2.0/nsdb/NucFeaturePackage/QualifierListHelper.java
-act-2.0/nsdb/NucFeaturePackage/Qualifier.class
-act-2.0/nsdb/NucFeaturePackage/QualifierValue_u.class
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-act-2.0/nsdb/NucFeaturePackage/QualifierHelper.class
-act-2.0/nsdb/NucFeaturePackage/QualifierValue_uHelper.class
-act-2.0/nsdb/NucFeaturePackage/QualifierValueListHelper.class
-act-2.0/nsdb/NucSeq.java
-act-2.0/nsdb/NucSeqOperations.java
-act-2.0/nsdb/NucSeqHelper.java
-act-2.0/nsdb/NucSeqHolder.java
-act-2.0/nsdb/_NucSeqStub.java
-act-2.0/nsdb/NucSeqPOA.java
-act-2.0/nsdb/NucSeqPOATie.java
-act-2.0/nsdb/Embl.java
-act-2.0/nsdb/EmblSeq.java
-act-2.0/nsdb/EmblSeqOperations.java
-act-2.0/nsdb/EmblSeqHelper.java
-act-2.0/nsdb/EmblSeqHolder.java
-act-2.0/nsdb/_EmblSeqStub.java
-act-2.0/nsdb/EmblSeqPOA.java
-act-2.0/nsdb/EmblSeqPOATie.java
-act-2.0/nsdb/EmblOperations.java
-act-2.0/nsdb/EmblHelper.java
-act-2.0/nsdb/EmblHolder.java
-act-2.0/nsdb/_EmblStub.java
-act-2.0/nsdb/EmblPOA.java
-act-2.0/nsdb/EmblPOATie.java
-act-2.0/nsdb/EmblPackage/Superceded.java
-act-2.0/nsdb/EmblPackage/SupercededHolder.java
-act-2.0/nsdb/EmblPackage/SupercededHelper.java
-act-2.0/nsdb/EmblPackage/Superceded.class
-act-2.0/nsdb/EmblPackage/SupercededHelper.class
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-act-2.0/nsdb/LocationParse.java
-act-2.0/nsdb/OutOfDateHolder.java
-act-2.0/nsdb/OutOfDateHelper.java
-act-2.0/nsdb/ReadOnlyException.java
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-act-2.0/nsdb/NucFeatureWriterListHolder.java
-act-2.0/nsdb/Embl.class
-act-2.0/nsdb/NucFeatureWriterListHelper.java
-act-2.0/nsdb/datestamp_tHelper.java
-act-2.0/nsdb/Datestamp.java
-act-2.0/nsdb/DatestampHolder.java
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-act-2.0/nsdb/EntryStats.java
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-act-2.0/nsdb/ServerInfo.java
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-act-2.0/nsdb/InvalidKey.java
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-act-2.0/nsdb/CommitFailed.java
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-act-2.0/nsdb/EmblSeqWriter.java
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-act-2.0/seqdb/BioSeq.java
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-act-2.0/seqdb/BioSeqHelper.java
-act-2.0/seqdb/BioSeqHolder.java
-act-2.0/seqdb/_BioSeqStub.java
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-act-2.0/seqdb/Feature.class
-act-2.0/Ensembl/artemis/RequestedSequenceTooLong.java
-act-2.0/Ensembl/artemis/RequestedSequenceTooLongHolder.java
-act-2.0/Ensembl/artemis/RequestedSequenceTooLongHelper.java
-act-2.0/Ensembl/artemis/NoEntry.java
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-act-2.0/Ensembl/artemis/QualifierListHolder.java
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-act-2.0/Ensembl/artemis/_FeatureStub.java
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-act-2.0/Ensembl/artemis/DB.java
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-act-2.0/Ensembl/artemis/FeatureListHolder.java
-act-2.0/Ensembl/artemis/FeatureListHelper.java
-act-2.0/Ensembl/artemis/Entry.java
-act-2.0/Ensembl/artemis/EntryOperations.java
-act-2.0/Ensembl/artemis/EntryHelper.java
-act-2.0/Ensembl/artemis/EntryHolder.java
-act-2.0/Ensembl/artemis/_EntryStub.java
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-act-2.0/Ensembl/artemis/FeatureDefinitionListHolder.java
-act-2.0/Ensembl/artemis/FeatureDefinitionListHelper.java
-act-2.0/Ensembl/artemis/EntryNameListHolder.java
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-act-2.0/Ensembl/artemis/DBOperations.java
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-act-2.0/Ensembl/artemis/_DBStub.java
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-act-2.0/Dad.class
-act-2.0/AppGlobal.class
-bin/act
-@dirrm act-2.0/CVS
-@dirrm act-2.0/META-INF/CVS
-@dirrm act-2.0/META-INF
-@dirrm act-2.0/diana/CVS
-@dirrm act-2.0/diana/plot/CVS
-@dirrm act-2.0/diana/plot
-@dirrm act-2.0/diana/components/CVS
-@dirrm act-2.0/diana/components
-@dirrm act-2.0/diana/sequence/CVS
-@dirrm act-2.0/diana/sequence
-@dirrm act-2.0/diana
-@dirrm act-2.0/corba/CVS
-@dirrm act-2.0/corba
-@dirrm act-2.0/etc/CVS
-@dirrm act-2.0/etc
-@dirrm act-2.0/uk/CVS
-@dirrm act-2.0/uk/ac/CVS
-@dirrm act-2.0/uk/ac/sanger/CVS
-@dirrm act-2.0/uk/ac/sanger/pathogens/CVS
-@dirrm act-2.0/uk/ac/sanger/pathogens/embl/CVS
-@dirrm act-2.0/uk/ac/sanger/pathogens/embl
-@dirrm act-2.0/uk/ac/sanger/pathogens
-@dirrm act-2.0/uk/ac/sanger
-@dirrm act-2.0/uk/ac
-@dirrm act-2.0/uk
-@dirrm act-2.0/lib/CVS
-@dirrm act-2.0/lib
-@dirrm act-2.0/collections/CVS
-@dirrm act-2.0/collections
-@dirrm act-2.0/type
-@dirrm act-2.0/nsdb/LocationPackage
-@dirrm act-2.0/nsdb/NucFeaturePackage
-@dirrm act-2.0/nsdb/EmblPackage
-@dirrm act-2.0/nsdb
-@dirrm act-2.0/seqdb
-@dirrm act-2.0/Ensembl/artemis
-@dirrm act-2.0/Ensembl
-@dirrm act-2.0