Date: Thu, 10 Jun 2004 19:36:14 -0300 (ART) From: Fernan Aguero <fernan@iib.unsam.edu.ar> To: FreeBSD-gnats-submit@FreeBSD.org Subject: ports/67811: [new port] biology/ariadne Message-ID: <200406102236.i5AMaE3q006392@pi.iib.unsam.edu.ar> Resent-Message-ID: <200406102250.i5AMoJ6b010503@freefall.freebsd.org>
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>Number: 67811 >Category: ports >Synopsis: [new port] biology/ariadne >Confidential: no >Severity: non-critical >Priority: low >Responsible: freebsd-ports-bugs >State: open >Quarter: >Keywords: >Date-Required: >Class: maintainer-update >Submitter-Id: current-users >Arrival-Date: Thu Jun 10 22:50:16 GMT 2004 >Closed-Date: >Last-Modified: >Originator: Fernan Aguero >Release: FreeBSD 4.10-RELEASE i386 >Organization: IIB-UNSAM >Environment: FreeBSD pi.iib.unsam.edu.ar 4.10-RELEASE FreeBSD 4.10-RELEASE #0: Wed May 26 12:56:43 ART 2004 fernan@pi.iib.unsam.edu.ar:/usr/obj/usr/src/sys/PI i386 >Description: A program to do Smith-Waterman alignments using a new accurate formula to assess statistical significance. >How-To-Repeat: >Fix: --- Makefile begins here --- # vim:ts=8:sw=8:number:nowrap # 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, using the Smith-Waterman algorithm WRKSRC= ${WRKDIR}/SRC-${PORTVERSION} USE_GMAKE= yes USE_REINPLACE= yes post-patch: @${REINPLACE_CMD} -e 's|-lpthread|${PTHREAD_LIBS}|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> --- Makefile ends here --- --- distinfo begins here --- MD5 (ariadne-1.3.tar.Z) = 240dc8b278a02b0fcdf56cd186d9b0ec SIZE (ariadne-1.3.tar.Z) = 69427 --- distinfo ends here --- --- pkg-descr begins here --- 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/ --- pkg-descr ends here --- --- pkg-plist begins here --- bin/ariadne bin/prospero share/doc/ariadne/README @dirrm share/doc/ariadne --- pkg-plist ends here --- >Release-Note: >Audit-Trail: >Unformatted:
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