diff options
| author | Kirill Ponomarev <krion@FreeBSD.org> | 2004-06-22 14:29:59 +0000 |
|---|---|---|
| committer | Kirill Ponomarev <krion@FreeBSD.org> | 2004-06-22 14:29:59 +0000 |
| commit | bd7a90118c9c14cb0ec41c88db6445bfdbf3ea06 (patch) | |
| tree | ac022520ecd36d7f1da2bfad1c3e4ddab7a9b856 /biology/ariadne | |
| parent | b76e9b7622d9f659d6b20beff08f8a5c1a10dc96 (diff) | |
| download | ports-bd7a90118c9c14cb0ec41c88db6445bfdbf3ea06.tar.gz ports-bd7a90118c9c14cb0ec41c88db6445bfdbf3ea06.zip | |
Add ariadne 1.3, programs to compare protein sequences and
profiles, using the Smith-Waterman algorithm.
PR: ports/67811
Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar>
Notes
Notes:
svn path=/head/; revision=111985
Diffstat (limited to 'biology/ariadne')
| -rw-r--r-- | biology/ariadne/Makefile | 35 | ||||
| -rw-r--r-- | biology/ariadne/distinfo | 2 | ||||
| -rw-r--r-- | biology/ariadne/pkg-descr | 18 | ||||
| -rw-r--r-- | biology/ariadne/pkg-plist | 4 |
4 files changed, 59 insertions, 0 deletions
diff --git a/biology/ariadne/Makefile b/biology/ariadne/Makefile new file mode 100644 index 000000000000..e477b5a3fd31 --- /dev/null +++ b/biology/ariadne/Makefile @@ -0,0 +1,35 @@ +# New ports collection makefile for: ariadne +# Date created: 10 Jun 2004 +# Whom: Fernan Aguero <fernan@iib.unsam.edu.ar> +# +# $FreeBSD$ +# + +PORTNAME= ariadne +PORTVERSION= 1.3 +CATEGORIES= biology +MASTER_SITES= http://www.well.ox.ac.uk/ariadne/ +EXTRACT_SUFX= .tar.Z + +MAINTAINER= fernan@iib.unsam.edu.ar +COMMENT= Programs to compare protein sequences and profiles + +WRKSRC= ${WRKDIR}/SRC-${PORTVERSION} +USE_GMAKE= yes +USE_REINPLACE= yes + +post-patch: + @${REINPLACE_CMD} -e 's|-lpthread|${PTHREAD_LIBS}| ; \ + s|CC =|CC ?=| ; \ + s|CFLAGS =|CFLAGS +=| ; \ + s|-c $(OPTIMISE)|-c $(CFLAGS) $(OPTIMIZE)|g' ${WRKSRC}/Makefile + +do-install: + ${INSTALL_PROGRAM} ${WRKSRC}/${OPSYS}/ariadne ${PREFIX}/bin + ${INSTALL_PROGRAM} ${WRKSRC}/${OPSYS}/prospero ${PREFIX}/bin +.if !defined(NOPORTDOCS) + @${MKDIR} ${DOCSDIR} + ${INSTALL_DATA} ${WRKSRC}/README ${DOCSDIR} +.endif + +.include <bsd.port.mk> diff --git a/biology/ariadne/distinfo b/biology/ariadne/distinfo new file mode 100644 index 000000000000..f7ceb4358242 --- /dev/null +++ b/biology/ariadne/distinfo @@ -0,0 +1,2 @@ +MD5 (ariadne-1.3.tar.Z) = 240dc8b278a02b0fcdf56cd186d9b0ec +SIZE (ariadne-1.3.tar.Z) = 69427 diff --git a/biology/ariadne/pkg-descr b/biology/ariadne/pkg-descr new file mode 100644 index 000000000000..e1df53602fbf --- /dev/null +++ b/biology/ariadne/pkg-descr @@ -0,0 +1,18 @@ +ARIADNE is a package of two programs, ariadne and prospero, that compare +protein sequences and profiles using the Smith-Waterman algorithm, and +assesses statistical significance using a new accurate formula, +described in Mott, 2000, "Accurate Formula for P-values of gapped local +sequence and profile alignments" J. Mol Biol. 300:649-659. + +The sequence/profile comparison algorithms used in ARIADNE are standard, +and are probably not the fastest implementations available. The novel +part is the method for determining statistical significance, which will +give thresholds of significance that are accurate to within 5% 95% of +the time. + +The package is written in ANSI C. You are free to incorporate the method +used for assessing statistical significance into third-party code, +provided you cite the above reference. The routines for assessing +significance are all in gaplib.c + +WWW: http://www.well.ox.ac.uk/ariadne/ diff --git a/biology/ariadne/pkg-plist b/biology/ariadne/pkg-plist new file mode 100644 index 000000000000..cc92b2c7ea50 --- /dev/null +++ b/biology/ariadne/pkg-plist @@ -0,0 +1,4 @@ +bin/ariadne +bin/prospero +%%PORTDOCS%%%%DOCSDIR%%/README +%%PORTDOCS%%@dirrm %%DOCSDIR%% |