ports/67811: [new port] biology/ariadne

[Fernan Aguero]

The following reply was made to PR ports/67811; it has been noted by GNATS.

From: Fernan Aguero <fernan at iib.unsam.edu.ar>
To: Kirill Ponomarew <krion at FreeBSD.org>
Cc: freebsd-ports-bugs at FreeBSD.org,
	FreeBSD GNATS PR Submission <freebsd-gnats-submit at FreeBSD.org>
Subject: Re: ports/67811: [new port] biology/ariadne
Date: Fri, 11 Jun 2004 13:44:11 -0300

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 +----[ Kirill Ponomarew <krion at FreeBSD.org> (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
 
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 Content-Type: application/x-shar
 Content-Disposition: attachment; filename="ariadne.shar"
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 # 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 <fernan at iib.unsam.edu.ar>=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 at 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 <bsd.port.mk>=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 at dirrm sh=
 are/doc/ariadne=0AEND-of-ariadne/pkg-plist=0Aexit=0A=0A
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