diff options
| -rw-r--r-- | biology/Makefile | 1 | ||||
| -rw-r--r-- | biology/act/Makefile | 33 | ||||
| -rw-r--r-- | biology/act/distinfo | 1 | ||||
| -rw-r--r-- | biology/act/pkg-comment | 1 | ||||
| -rw-r--r-- | biology/act/pkg-descr | 12 | ||||
| -rw-r--r-- | biology/act/pkg-plist | 983 |
6 files changed, 1031 insertions, 0 deletions
diff --git a/biology/Makefile b/biology/Makefile index 9a4012b..c93eaeb 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -2,6 +2,7 @@ # SUBDIR += L-Breeder + SUBDIR += act SUBDIR += artemis SUBDIR += avida SUBDIR += babel diff --git a/biology/act/Makefile b/biology/act/Makefile new file mode 100644 index 0000000..4c8b43f --- /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 0000000..48b3198 --- /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 0000000..0e5bfab --- /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 0000000..f610f95 --- /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 0000000..46e5a82 --- /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 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