diff options
| -rw-r--r-- | biology/Makefile | 1 | ||||
| -rw-r--r-- | biology/mummer/Makefile | 43 | ||||
| -rw-r--r-- | biology/mummer/distinfo | 3 | ||||
| -rw-r--r-- | biology/mummer/pkg-descr | 6 | ||||
| -rw-r--r-- | biology/mummer/pkg-plist | 26 |
5 files changed, 79 insertions, 0 deletions
diff --git a/biology/Makefile b/biology/Makefile index 6625014fe476..9cc884558da2 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -46,6 +46,7 @@ SUBDIR += migrate SUBDIR += molden SUBDIR += mopac + SUBDIR += mummer SUBDIR += nab SUBDIR += ncbi-toolkit SUBDIR += ortep3 diff --git a/biology/mummer/Makefile b/biology/mummer/Makefile new file mode 100644 index 000000000000..0b7a065c9eb7 --- /dev/null +++ b/biology/mummer/Makefile @@ -0,0 +1,43 @@ +# ex:ts=8 +# New ports collection makefile for: MUMmer +# Date created: 20 November 2007 +# Whom: Tony Maher +# +# $FreeBSD$ +# + +PORTNAME= mummer +PORTVERSION= 3.20 +CATEGORIES= biology +MASTER_SITES= SF +DISTNAME= MUMmer${PORTVERSION} + +MAINTAINER= Anthony.Maher@uts.edu.au +COMMENT= A modular system for rapid whole genome alignment + +USE_GMAKE= yes + +PROGRAMS= annotate combineMUMs delta-filter gaps \ + mgaps mummer repeat-match show-aligns \ + show-coords show-diff show-snps show-tiling +SCRIPTS= dnadiff exact-tandems mapview mummerplot nucmer \ + nucmer2xfig promer run-mummer1 run-mummer3 +DOCUMENTS= COPYRIGHT INSTALL LICENSE README + +do-install: +.for program in ${PROGRAMS} + (cd ${WRKSRC} && ${INSTALL_PROGRAM} ${program} ${PREFIX}/bin) +.endfor + +.for script in ${SCRIPTS} + (cd ${WRKSRC} && ${INSTALL_SCRIPT} ${script} ${PREFIX}/bin) +.endfor + +.if !defined(NOPORTDOCS) + @${MKDIR} ${DOCSDIR} +.for doc in ${DOCUMENTS} + (cd ${WRKSRC} && ${INSTALL_DATA} ${doc} ${DOCSDIR}) +.endfor +.endif + +.include <bsd.port.mk> diff --git a/biology/mummer/distinfo b/biology/mummer/distinfo new file mode 100644 index 000000000000..ef9cc2f7db58 --- /dev/null +++ b/biology/mummer/distinfo @@ -0,0 +1,3 @@ +MD5 (MUMmer3.20.tar.gz) = 4c3f6e528df50f8dfd3a7cd0ea224306 +SHA256 (MUMmer3.20.tar.gz) = 9c7880b4ce25ef3c6bed9ccdc26f1c4d7e74eb0ef1ce403907790c0f96c0f260 +SIZE (MUMmer3.20.tar.gz) = 3155446 diff --git a/biology/mummer/pkg-descr b/biology/mummer/pkg-descr new file mode 100644 index 000000000000..61b5d007a15f --- /dev/null +++ b/biology/mummer/pkg-descr @@ -0,0 +1,6 @@ +MUMmer is a modular system for the rapid whole genome alignment of finished +or draft sequence. This package provides an efficient suffix tree library, +seed-and-extend alignment, SNP detection, repeat detection, and +visualization tools. + +WWW: http://mummer.sourceforge.net/ diff --git a/biology/mummer/pkg-plist b/biology/mummer/pkg-plist new file mode 100644 index 000000000000..d569fa3bba7e --- /dev/null +++ b/biology/mummer/pkg-plist @@ -0,0 +1,26 @@ +bin/annotate +bin/combineMUMs +bin/delta-filter +bin/dnadiff +bin/exact-tandems +bin/gaps +bin/mapview +bin/mgaps +bin/mummer +bin/mummerplot +bin/nucmer +bin/nucmer2xfig +bin/promer +bin/repeat-match +bin/run-mummer1 +bin/run-mummer3 +bin/show-aligns +bin/show-coords +bin/show-diff +bin/show-snps +bin/show-tiling +%%PORTDOCS%%%%DOCSDIR%%/COPYRIGHT +%%PORTDOCS%%%%DOCSDIR%%/INSTALL +%%PORTDOCS%%%%DOCSDIR%%/LICENSE +%%PORTDOCS%%%%DOCSDIR%%/README +%%PORTDOCS%%@dirrm %%DOCSDIR%% |