New Port: biology/act

PR:		ports/35753
Submitted by:	Camson Huynh <chuynh@biolateral.com.au>

5 files changed, 1030 insertions, 0 deletions

diff --git a/biology/act/Makefile b/biology/act/Makefile
new file mode 100644
index 000000000000..4c8b43fc33c0
--- /dev/null
+++ b/biology/act/Makefile
@@ -0,0 +1,33 @@
+# New ports collection makefile for:	artemis
+# Date created:				11 Mar 2002
+# Whom:					chuynh@bilateral.com.au
+#
+# $FreeBSD$
+#
+
+PORTNAME=	act
+PORTVERSION=	1.0
+CATEGORIES=	biology
+MASTER_SITES=	http://www.sanger.ac.uk/Software/ACT/v1/
+DISTNAME=	act_compiled_v1
+
+MAINTAINER=	chuynh@biolateral.com.au
+
+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
new file mode 100644
index 000000000000..48b31986c4a9
--- /dev/null
+++ b/biology/act/distinfo
@@ -0,0 +1 @@
+MD5 (act_compiled_v1.tar.gz) = 30e263c6507007d866a24b59c0767d77
diff --git a/biology/act/pkg-comment b/biology/act/pkg-comment
new file mode 100644
index 000000000000..0e5bfabd633a
--- /dev/null
+++ b/biology/act/pkg-comment
@@ -0,0 +1 @@
+A DNA sequence comparison viewer based on Artemis
diff --git a/biology/act/pkg-descr b/biology/act/pkg-descr
new file mode 100644
index 000000000000..f610f9519091
--- /dev/null
+++ b/biology/act/pkg-descr
@@ -0,0 +1,12 @@
+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
new file mode 100644
index 000000000000..46e5a821c9db
--- /dev/null
+++ b/biology/act/pkg-plist
@@ -0,0 +1,983 @@
+act-1.0/CVS/Root
+act-1.0/CVS/Repository
+act-1.0/CVS/Entries
+act-1.0/.cvsignore
+act-1.0/AppGlobal.java
+act-1.0/Dad.java
+act-1.0/Makefile
+act-1.0/act
+act-1.0/META-INF/CVS/Root
+act-1.0/META-INF/CVS/Repository
+act-1.0/META-INF/CVS/Entries
+act-1.0/META-INF/MANIFEST.MF
+act-1.0/uk/CVS/Root
+act-1.0/uk/CVS/Repository
+act-1.0/uk/CVS/Entries
+act-1.0/uk/ac/CVS/Root
+act-1.0/uk/ac/CVS/Repository
+act-1.0/uk/ac/CVS/Entries
+act-1.0/uk/ac/sanger/CVS/Root
+act-1.0/uk/ac/sanger/CVS/Repository
+act-1.0/uk/ac/sanger/CVS/Entries
+act-1.0/uk/ac/sanger/pathogens/CVS/Root
+act-1.0/uk/ac/sanger/pathogens/CVS/Repository
+act-1.0/uk/ac/sanger/pathogens/CVS/Entries
+act-1.0/uk/ac/sanger/pathogens/Document.java
+act-1.0/uk/ac/sanger/pathogens/FastVector.java
+act-1.0/uk/ac/sanger/pathogens/FileDocument.java
+act-1.0/uk/ac/sanger/pathogens/FileProgressDocument.java
+act-1.0/uk/ac/sanger/pathogens/InputStreamProgressEvent.java
+act-1.0/uk/ac/sanger/pathogens/InputStreamProgressListener.java
+act-1.0/uk/ac/sanger/pathogens/OutOfRangeException.java
+act-1.0/uk/ac/sanger/pathogens/ProgressInputStream.java
+act-1.0/uk/ac/sanger/pathogens/ReadOnlyException.java
+act-1.0/uk/ac/sanger/pathogens/StringVector.java
+act-1.0/uk/ac/sanger/pathogens/URLDocument.java
+act-1.0/uk/ac/sanger/pathogens/embl/CVS/Root
+act-1.0/uk/ac/sanger/pathogens/embl/CVS/Repository
+act-1.0/uk/ac/sanger/pathogens/embl/CVS/Entries
+act-1.0/uk/ac/sanger/pathogens/embl/BetweenRange.java
+act-1.0/uk/ac/sanger/pathogens/embl/ComparableFeature.java
+act-1.0/uk/ac/sanger/pathogens/embl/CorbaEntry.java
+act-1.0/uk/ac/sanger/pathogens/embl/CorbaFeature.java
+act-1.0/uk/ac/sanger/pathogens/embl/CorbaSequence.java
+act-1.0/uk/ac/sanger/pathogens/embl/DateStampFeature.java
+act-1.0/uk/ac/sanger/pathogens/embl/DocumentEntry.java
+act-1.0/uk/ac/sanger/pathogens/embl/DocumentEntryAutosaveThread.java
+act-1.0/uk/ac/sanger/pathogens/embl/DocumentEntryFactory.java
+act-1.0/uk/ac/sanger/pathogens/embl/DocumentFeature.java
+act-1.0/uk/ac/sanger/pathogens/embl/EMBLObject.java
+act-1.0/uk/ac/sanger/pathogens/embl/Entry.java
+act-1.0/uk/ac/sanger/pathogens/embl/EmblDocumentEntry.java
+act-1.0/uk/ac/sanger/pathogens/embl/EmblMisc.java
+act-1.0/uk/ac/sanger/pathogens/embl/EmblStreamFeature.java
+act-1.0/uk/ac/sanger/pathogens/embl/EmblStreamSequence.java
+act-1.0/uk/ac/sanger/pathogens/embl/EnsemblCorbaEntry.java
+act-1.0/uk/ac/sanger/pathogens/embl/EnsemblCorbaFeature.java
+act-1.0/uk/ac/sanger/pathogens/embl/EnsemblCorbaSequence.java
+act-1.0/uk/ac/sanger/pathogens/embl/EntryInformation.java
+act-1.0/uk/ac/sanger/pathogens/embl/EntryInformationException.java
+act-1.0/uk/ac/sanger/pathogens/embl/FastaStreamSequence.java
+act-1.0/uk/ac/sanger/pathogens/embl/Feature.java
+act-1.0/uk/ac/sanger/pathogens/embl/FeatureComparator.java
+act-1.0/uk/ac/sanger/pathogens/embl/Key.java
+act-1.0/uk/ac/sanger/pathogens/embl/FeatureEnumeration.java
+act-1.0/uk/ac/sanger/pathogens/embl/FeatureHeader.java
+act-1.0/uk/ac/sanger/pathogens/embl/FeatureTable.java
+act-1.0/uk/ac/sanger/pathogens/embl/FeatureTree.java
+act-1.0/uk/ac/sanger/pathogens/embl/FeatureVector.java
+act-1.0/uk/ac/sanger/pathogens/embl/FuzzyRange.java
+act-1.0/uk/ac/sanger/pathogens/embl/GFFDocumentEntry.java
+act-1.0/uk/ac/sanger/pathogens/embl/GFFMisc.java
+act-1.0/uk/ac/sanger/pathogens/embl/GFFEntryInformation.java
+act-1.0/uk/ac/sanger/pathogens/embl/GFFStreamFeature.java
+act-1.0/uk/ac/sanger/pathogens/embl/GenbankDocumentEntry.java
+act-1.0/uk/ac/sanger/pathogens/embl/GenbankMisc.java
+act-1.0/uk/ac/sanger/pathogens/embl/GenbankStreamFeature.java
+act-1.0/uk/ac/sanger/pathogens/embl/GenbankStreamSequence.java
+act-1.0/uk/ac/sanger/pathogens/embl/InvalidKeyException.java
+act-1.0/uk/ac/sanger/pathogens/embl/InvalidQualifierException.java
+act-1.0/uk/ac/sanger/pathogens/embl/InvalidRelationException.java
+act-1.0/uk/ac/sanger/pathogens/embl/KeyVector.java
+act-1.0/uk/ac/sanger/pathogens/embl/LineGroup.java
+act-1.0/uk/ac/sanger/pathogens/embl/LineGroupVector.java
+act-1.0/uk/ac/sanger/pathogens/embl/LinePushBackReader.java
+act-1.0/uk/ac/sanger/pathogens/embl/Location.java
+act-1.0/uk/ac/sanger/pathogens/embl/LocationLexer.java
+act-1.0/uk/ac/sanger/pathogens/embl/Qualifier.java
+act-1.0/uk/ac/sanger/pathogens/embl/LocationParseException.java
+act-1.0/uk/ac/sanger/pathogens/embl/LocationParseNode.java
+act-1.0/uk/ac/sanger/pathogens/embl/LocationParseNodeVector.java
+act-1.0/uk/ac/sanger/pathogens/embl/LowerInteger.java
+act-1.0/uk/ac/sanger/pathogens/embl/MSPcrunchDocumentEntry.java
+act-1.0/uk/ac/sanger/pathogens/embl/MSPcrunchEntryInformation.java
+act-1.0/uk/ac/sanger/pathogens/embl/MSPcrunchStreamFeature.java
+act-1.0/uk/ac/sanger/pathogens/embl/MiscLineGroup.java
+act-1.0/uk/ac/sanger/pathogens/embl/OutOfDateException.java
+act-1.0/uk/ac/sanger/pathogens/embl/PublicDBDocumentEntry.java
+act-1.0/uk/ac/sanger/pathogens/embl/PublicDBStreamFeature.java
+act-1.0/uk/ac/sanger/pathogens/embl/PushBackException.java
+act-1.0/uk/ac/sanger/pathogens/embl/QualifierInfo.java
+act-1.0/uk/ac/sanger/pathogens/embl/QualifierInfoException.java
+act-1.0/uk/ac/sanger/pathogens/embl/QualifierInfoVector.java
+act-1.0/uk/ac/sanger/pathogens/embl/QualifierParseException.java
+act-1.0/uk/ac/sanger/pathogens/embl/QualifierVector.java
+act-1.0/uk/ac/sanger/pathogens/embl/RWCorbaEntry.java
+act-1.0/uk/ac/sanger/pathogens/embl/RWCorbaFeature.java
+act-1.0/uk/ac/sanger/pathogens/embl/Range.java
+act-1.0/uk/ac/sanger/pathogens/embl/RangeVector.java
+act-1.0/uk/ac/sanger/pathogens/embl/RawStreamSequence.java
+act-1.0/uk/ac/sanger/pathogens/embl/ReadFormatException.java
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+act-1.0/diana/plot/CodonWeight.java
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+act-1.0/diana/plot/HydroAlgorithm.java
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+act-1.0/diana/ExternalSearchProgram.java
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+act-1.0/diana/FeatureSegment.java
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+act-1.0/diana/MUMmerComparisonData.java
+act-1.0/diana/Options.java
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