From owner-freebsd-ports-bugs@FreeBSD.ORG Fri Jun 11 16:50:41 2004 Return-Path: Delivered-To: freebsd-ports-bugs@hub.freebsd.org Received: from mx1.FreeBSD.org (mx1.freebsd.org [216.136.204.125]) by hub.freebsd.org (Postfix) with ESMTP id 8325B16A4CE for ; Fri, 11 Jun 2004 16:50:41 +0000 (GMT) Received: from freefall.freebsd.org (freefall.freebsd.org [216.136.204.21]) by mx1.FreeBSD.org (Postfix) with ESMTP id 679F143D5D for ; Fri, 11 Jun 2004 16:50:41 +0000 (GMT) (envelope-from gnats@FreeBSD.org) Received: from freefall.freebsd.org (gnats@localhost [127.0.0.1]) i5BGoRKv018989 for ; Fri, 11 Jun 2004 16:50:27 GMT (envelope-from gnats@freefall.freebsd.org) Received: (from gnats@localhost) by freefall.freebsd.org (8.12.11/8.12.11/Submit) id i5BGoR23018988; Fri, 11 Jun 2004 16:50:27 GMT (envelope-from gnats) Date: Fri, 11 Jun 2004 16:50:27 GMT Message-Id: <200406111650.i5BGoR23018988@freefall.freebsd.org> To: freebsd-ports-bugs@FreeBSD.org From: Fernan Aguero Subject: Re: ports/67811: [new port] biology/ariadne X-BeenThere: freebsd-ports-bugs@freebsd.org X-Mailman-Version: 2.1.1 Precedence: list Reply-To: Fernan Aguero List-Id: Ports bug reports List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Fri, 11 Jun 2004 16:50:41 -0000 The following reply was made to PR ports/67811; it has been noted by GNATS. From: Fernan Aguero To: Kirill Ponomarew Cc: freebsd-ports-bugs@FreeBSD.org, FreeBSD GNATS PR Submission Subject: Re: ports/67811: [new port] biology/ariadne Date: Fri, 11 Jun 2004 13:44:11 -0300 --WIyZ46R2i8wDzkSu Content-Type: text/plain; charset=us-ascii Content-Disposition: inline +----[ Kirill Ponomarew (11.Jun.2004 07:35): | | Synopsis: [new port] biology/ariadne | | State-Changed-From-To: open->feedback | State-Changed-By: krion | State-Changed-When: Fri Jun 11 10:12:15 GMT 2004 | State-Changed-Why: | Please use shar(1) for submitting new ports. | | http://www.freebsd.org/cgi/query-pr.cgi?pr=67811 | +----] Sorry, I forgot about that. Here is the shar archive containing the port's files. Fernan -- F e r n a n A g u e r o http://genoma.unsam.edu.ar/~fernan --WIyZ46R2i8wDzkSu Content-Type: application/x-shar Content-Disposition: attachment; filename="ariadne.shar" Content-Transfer-Encoding: quoted-printable # This is a shell archive. Save it in a file, remove anything before=0A# t= his line, and then unpack it by entering "sh file". Note, it may=0A# creat= e directories; files and directories will be owned by you and=0A# have defa= ult permissions.=0A#=0A# This archive contains:=0A#=0A# ariadne=0A# ariadne= /distinfo=0A# ariadne/pkg-descr=0A# ariadne/Makefile=0A# ariadne/pkg-plist= =0A#=0Aecho c - ariadne=0Amkdir -p ariadne > /dev/null 2>&1=0Aecho x - aria= dne/distinfo=0Ased 's/^X//' >ariadne/distinfo << 'END-of-ariadne/distinfo'= =0AXMD5 (ariadne-1.3.tar.Z) =3D 240dc8b278a02b0fcdf56cd186d9b0ec=0AXSIZE (a= riadne-1.3.tar.Z) =3D 69427=0AEND-of-ariadne/distinfo=0Aecho x - ariadne/pk= g-descr=0Ased 's/^X//' >ariadne/pkg-descr << 'END-of-ariadne/pkg-descr'=0AX= ARIADNE is a package of two programs, ariadne and prospero, that compare=0A= Xprotein sequences and profiles using the Smith-Waterman algorithm, and=0AX= assesses statistical significance using a new accurate formula,=0AXdescribe= d in Mott, 2000, "Accurate Formula for P-values of gapped local=0AXsequence= and profile alignments" J. Mol Biol. 300:649-659.=0AX=0AXThe sequence/prof= ile comparison algorithms used in ARIADNE are standard,=0AXand are probably= not the fastest implementations available. The novel=0AXpart is the method= for determining statistical significance, which will=0AXgive thresholds of= significance that are accurate to within 5% 95% of=0AXthe time.=0AX=0AXThe= package is written in ANSI C. You are free to incorporate the method=0AXus= ed for assessing statistical significance into third-party code,=0AXprovide= d you cite the above reference. The routines for assessing=0AXsignificance = are all in gaplib.c =0AX=0AXWWW: http://www.well.ox.ac.uk/ariadne/=0AEND-of= -ariadne/pkg-descr=0Aecho x - ariadne/Makefile=0Ased 's/^X//' >ariadne/Make= file << 'END-of-ariadne/Makefile'=0AX# vim:ts=3D8:sw=3D8:number:nowrap=0AX#= New ports collection makefile for: ariadne=0AX# Date created: 10 Jun 2004= =0AX# Whom: Fernan Aguero =0AX#=0AX# $Free= BSD$=0AX#=0AX=0AXPORTNAME=3D ariadne=0AXPORTVERSION=3D 1.3=0AXCATEGORIES=3D= biology=0AXMASTER_SITES=3D http://www.well.ox.ac.uk/ariadne/=0AXEXTRACT_SU= FX=3D .tar.Z=0AX=0AXMAINTAINER=3D fernan@iib.unsam.edu.ar=0AXCOMMENT=3D Pro= grams to compare protein sequences and profiles, using the Smith-Waterman a= lgorithm=0AX=0AXWRKSRC=3D ${WRKDIR}/SRC-${PORTVERSION}=0AXUSE_GMAKE=3D yes= =0AXUSE_REINPLACE=3D yes=0AX=0AXpost-patch:=0AX @${REINPLACE_CMD} -e 's|-lp= thread|${PTHREAD_LIBS}|g' ${WRKSRC}/Makefile=0AX=0AXdo-install:=0AX ${INSTA= LL_PROGRAM} ${WRKSRC}/${OPSYS}/ariadne ${PREFIX}/bin=0AX ${INSTALL_PROGRAM}= ${WRKSRC}/${OPSYS}/prospero ${PREFIX}/bin=0AX.if !defined(NOPORTDOCS)=0AX = @${MKDIR} ${DOCSDIR}=0AX ${INSTALL_DATA} ${WRKSRC}/README ${DOCSDIR}/=0AX.e= ndif=0AX=0AX.include =0AEND-of-ariadne/Makefile=0Aecho x - ari= adne/pkg-plist=0Ased 's/^X//' >ariadne/pkg-plist << 'END-of-ariadne/pkg-pli= st'=0AXbin/ariadne=0AXbin/prospero=0AXshare/doc/ariadne/README=0AX@dirrm sh= are/doc/ariadne=0AEND-of-ariadne/pkg-plist=0Aexit=0A=0A --WIyZ46R2i8wDzkSu--