diff options
| -rw-r--r-- | biology/Makefile | 1 | ||||
| -rw-r--r-- | biology/artemis/Makefile | 33 | ||||
| -rw-r--r-- | biology/artemis/distinfo | 1 | ||||
| -rw-r--r-- | biology/artemis/pkg-comment | 1 | ||||
| -rw-r--r-- | biology/artemis/pkg-descr | 7 | ||||
| -rw-r--r-- | biology/artemis/pkg-plist | 1486 |
6 files changed, 1529 insertions, 0 deletions
diff --git a/biology/Makefile b/biology/Makefile index d07fc1553357..b1798bf04f78 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -1,6 +1,7 @@ # $FreeBSD$ # + SUBDIR += artemis SUBDIR += babel SUBDIR += biojava SUBDIR += chemeq diff --git a/biology/artemis/Makefile b/biology/artemis/Makefile new file mode 100644 index 000000000000..58af9beae029 --- /dev/null +++ b/biology/artemis/Makefile @@ -0,0 +1,33 @@ +# New ports collection makefile for: artemis +# Date created: 10 Nov 2001 +# Whom: camson@bilateral.com.au +# +# $FreeBSD$ +# + +PORTNAME= artemis +PORTVERSION= 4.0 +CATEGORIES= biology +MASTER_SITES= http://www.sanger.ac.uk/Software/Artemis/v4/ +DISTNAME= artemis_compiled_v4 + +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}/art ${PREFIX}/bin/art + +PLIST_SUB= PORTVERSION="${PORTVERSION}" + +.include <bsd.port.mk> diff --git a/biology/artemis/distinfo b/biology/artemis/distinfo new file mode 100644 index 000000000000..dfad7f95ddd1 --- /dev/null +++ b/biology/artemis/distinfo @@ -0,0 +1 @@ +MD5 (artemis_compiled_v4.tar.gz) = e970b57e993a6b6d254ae70f83e1304e diff --git a/biology/artemis/pkg-comment b/biology/artemis/pkg-comment new file mode 100644 index 000000000000..26b8a15a2327 --- /dev/null +++ b/biology/artemis/pkg-comment @@ -0,0 +1 @@ +A DNA sequence viewer and annotation tool diff --git a/biology/artemis/pkg-descr b/biology/artemis/pkg-descr new file mode 100644 index 000000000000..7aed26ffa578 --- /dev/null +++ b/biology/artemis/pkg-descr @@ -0,0 +1,7 @@ +Artemis is a DNA sequence viewer and annotation tool that allows visualisation +of sequence features and the results of analyses within the context of the +sequence, and its six-frame translation. Artemis is written in Java, reads +EMBL or GENBANK format sequences and feature tables, and can work on sequences +of any size. + +WWW: http://www.sanger.ac.uk/Software/Artemis/manual diff --git a/biology/artemis/pkg-plist b/biology/artemis/pkg-plist new file mode 100644 index 000000000000..03ec13e72536 --- /dev/null +++ b/biology/artemis/pkg-plist @@ -0,0 +1,1486 @@ +artemis-4.0/CVS/Root +artemis-4.0/CVS/Repository +artemis-4.0/CVS/Entries +artemis-4.0/.cvsignore +artemis-4.0/AppGlobal.java +artemis-4.0/COPYING +artemis-4.0/COPYING.JacORB +artemis-4.0/CorbaApplet.java +artemis-4.0/Diana.java +artemis-4.0/INSTALL +artemis-4.0/Makefile +artemis-4.0/README +artemis-4.0/art +artemis-4.0/art.bat +artemis-4.0/mart +artemis-4.0/results_to_netscape +artemis-4.0/run_blast +artemis-4.0/run_blastn +artemis-4.0/run_blastp +artemis-4.0/run_blastx +artemis-4.0/run_fasta +artemis-4.0/run_hth +artemis-4.0/run_jalview +artemis-4.0/run_sigcleave +artemis-4.0/run_tblastn +artemis-4.0/run_tblastx +artemis-4.0/META-INF/CVS/Root +artemis-4.0/META-INF/CVS/Repository +artemis-4.0/META-INF/CVS/Entries +artemis-4.0/META-INF/MANIFEST.MF +artemis-4.0/collections/CVS/Root +artemis-4.0/collections/CVS/Repository +artemis-4.0/collections/CVS/Entries +artemis-4.0/collections/ArrayEnumeration.java +artemis-4.0/collections/Assertable.java +artemis-4.0/collections/Bag.java +artemis-4.0/collections/BinaryFunction.java +artemis-4.0/collections/CEImpl.java +artemis-4.0/collections/CLCell.java +artemis-4.0/collections/CLEnumeration.java +artemis-4.0/collections/Cell.java +artemis-4.0/collections/CheckedBag.java +artemis-4.0/collections/CheckedCollection.java +artemis-4.0/collections/CheckedMap.java +artemis-4.0/collections/CheckedSeq.java +artemis-4.0/collections/CheckedSet.java +artemis-4.0/collections/Keyed.java +artemis-4.0/collections/CircularList.java +artemis-4.0/collections/Collection.java +artemis-4.0/collections/CollectionEnumeration.java +artemis-4.0/collections/Comparator.java +artemis-4.0/collections/Dynarray.java +artemis-4.0/collections/CorruptedEnumerationException.java +artemis-4.0/collections/DAEnumeration.java +artemis-4.0/collections/DefaultComparator.java +artemis-4.0/collections/DefaultImplementations.java +artemis-4.0/collections/ElementSortedCollection.java +artemis-4.0/collections/FilteringEnumeration.java +artemis-4.0/collections/Function.java +artemis-4.0/collections/HTEnumeration.java +artemis-4.0/collections/HTPairEnumeration.java +artemis-4.0/collections/HashTableParams.java +artemis-4.0/collections/HashedMap.java +artemis-4.0/collections/HashedSet.java +artemis-4.0/collections/IllegalElementException.java +artemis-4.0/collections/Immutable.java +artemis-4.0/collections/ImplementationCheckable.java +artemis-4.0/collections/IncrBag.java +artemis-4.0/collections/ImplementationError.java +artemis-4.0/collections/IncrCollectionEnumeration.java +artemis-4.0/collections/IncrImpl.java +artemis-4.0/collections/IncrMap.java +artemis-4.0/collections/IncrSeq.java +artemis-4.0/collections/IncrSet.java +artemis-4.0/collections/InterleavingEnumeration.java +artemis-4.0/collections/KeySortedCollection.java +artemis-4.0/collections/LBEnumeration.java +artemis-4.0/collections/LLCell.java +artemis-4.0/collections/LLCellEnumeration.java +artemis-4.0/collections/LLMap.java +artemis-4.0/collections/LLPair.java +artemis-4.0/collections/LLPairEnumeration.java +artemis-4.0/collections/LinkedBuffer.java +artemis-4.0/collections/LinkedList.java +artemis-4.0/collections/Map.java +artemis-4.0/collections/MappingEnumeration.java +artemis-4.0/collections/Pair.java +artemis-4.0/collections/Predicate.java +artemis-4.0/collections/Procedure.java +artemis-4.0/collections/RBCell.java +artemis-4.0/collections/RBCellEnumeration.java +artemis-4.0/collections/RBMap.java +artemis-4.0/collections/RBPair.java +artemis-4.0/collections/RBPairEnumeration.java +artemis-4.0/collections/RBTree.java +artemis-4.0/collections/Seq.java +artemis-4.0/collections/Set.java +artemis-4.0/collections/SimpleTest.java +artemis-4.0/collections/SortableCollection.java +artemis-4.0/collections/UpdatableBag.java +artemis-4.0/collections/UpdatableBagImpl.java +artemis-4.0/collections/UpdatableCollection.java +artemis-4.0/collections/UpdatableImpl.java +artemis-4.0/collections/UpdatableMap.java +artemis-4.0/collections/UpdatableMapImpl.java +artemis-4.0/collections/javaMake +artemis-4.0/collections/UpdatableSeq.java +artemis-4.0/collections/UpdatableSeqImpl.java +artemis-4.0/collections/UpdatableSet.java +artemis-4.0/collections/UpdatableSetImpl.java +artemis-4.0/collections/collections_Dynarray.h +artemis-4.0/collections/Dynarray.class +artemis-4.0/collections/UpdatableSeqImpl.class +artemis-4.0/collections/UpdatableSeq.class +artemis-4.0/collections/SortableCollection.class +artemis-4.0/collections/Seq.class +artemis-4.0/collections/UpdatableImpl.class +artemis-4.0/collections/UpdatableCollection.class +artemis-4.0/collections/IllegalElementException.class +artemis-4.0/collections/CorruptedEnumerationException.class +artemis-4.0/collections/ImplementationError.class +artemis-4.0/collections/Collection.class +artemis-4.0/collections/Assertable.class +artemis-4.0/collections/ImplementationCheckable.class +artemis-4.0/collections/Comparator.class +artemis-4.0/collections/Predicate.class +artemis-4.0/collections/CollectionEnumeration.class +artemis-4.0/collections/DAEnumeration.class +artemis-4.0/collections/CEImpl.class +artemis-4.0/collections/KeySortedCollection.class +artemis-4.0/collections/Map.class +artemis-4.0/collections/ElementSortedCollection.class +artemis-4.0/collections/Bag.class +artemis-4.0/collections/Set.class +artemis-4.0/collections/RBTree.class +artemis-4.0/collections/UpdatableBagImpl.class +artemis-4.0/collections/UpdatableBag.class +artemis-4.0/collections/RBCell.class +artemis-4.0/collections/Cell.class +artemis-4.0/collections/DefaultComparator.class 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