ports/93055: [ new port ] biology/dotter

[Fernan Aguero]

>Number:         93055
>Category:       ports
>Synopsis:       [ new port ] biology/dotter
>Confidential:   no
>Severity:       non-critical
>Priority:       low
>Responsible:    freebsd-ports-bugs
>State:          open
>Quarter:        
>Keywords:       
>Date-Required:
>Class:          change-request
>Submitter-Id:   current-users
>Arrival-Date:   Wed Feb 08 19:20:06 GMT 2006
>Closed-Date:
>Last-Modified:
>Originator:     Fernan Aguero
>Release:        FreeBSD 6.0-RELEASE-p4 i386
>Organization:
IIB-UNSAM
>Environment:

System: FreeBSD omega.iib.unsam.edu.ar 6.0-RELEASE-p4 FreeBSD 6.0-RELEASE-p4 #0: Wed Jan 25 12:43:39 ART 2006 fernan at omega.iib.unsam.edu.ar:/usr/obj/usr/src/sys/OMEGA i386

	
>Description:
	

	See COMMENT and pkg-descr
	
>How-To-Repeat:
	
	
>Fix:

	



--- dotter.shar begins here ---
# This is a shell archive.  Save it in a file, remove anything before
# this line, and then unpack it by entering "sh file".  Note, it may
# create directories; files and directories will be owned by you and
# have default permissions.
#
# This archive contains:
#
#	dotter
#	dotter/Makefile
#	dotter/distinfo
#	dotter/pkg-descr
#
echo c - dotter
mkdir -p dotter > /dev/null 2>&1
echo x - dotter/Makefile
sed 's/^X//' >dotter/Makefile << 'END-of-dotter/Makefile'
X# ex:ts=8
X# New ports collection makefile for:	dotter
X# Date created:				11 Jan 2006
X# Whom:					Fernan Aguero <fernan at iib.unsam.edu.ar>
X#
X# $FreeBSD$
X#
X
XPORTNAME=	dotter
XPORTVERSION=	20021204 # last modified date in FTP server
XCATEGORIES=	biology
XMASTER_SITES=	ftp://ftp.cgb.ki.se/pub/esr/dotter/
XEXTRACT_SUFX=	#
XEXTRACT_ONLY=	#
XDIST_SUBDIR=	${PORTNAME}-${PORTVERSION}
X
XMAINTAINER=	fernan at iib.unsam.edu.ar
XCOMMENT=	A viewer for multiple sequence alignments
X
X.include <bsd.port.pre.mk>
X
X.if ${ARCH} == "i386"
XDISTNAME=	${PORTNAME}.LIN
XUSE_LINUX=	yes
X.else
XIGNORE=		There are also executables for Alpha and Sparc \
X		but they are for OSF and Solaris ... do they  \
X		run on FreeBSD-Sparc and FreeBSD-alpha?
X.endif
X
XNO_BUILD=	yes
XPLIST_FILES=	bin/${PORTNAME} bin/${DISTNAME}
X
Xdo-install:
X	${BRANDELF} -t Linux ${DISTDIR}/${DIST_SUBDIR}/${DISTNAME}
X	${INSTALL_PROGRAM} ${DISTDIR}/${DIST_SUBDIR}/${DISTNAME} \
X	${PREFIX}/bin
X	( cd ${PREFIX}/bin && ${LN} -s ${DISTNAME} ${PORTNAME} )
X
X.include <bsd.port.post.mk>
END-of-dotter/Makefile
echo x - dotter/distinfo
sed 's/^X//' >dotter/distinfo << 'END-of-dotter/distinfo'
XMD5 (dotter-20021204/dotter.LIN) = a308eb0b710b5e3e741ee09bd4b0982e
XSHA256 (dotter-20021204/dotter.LIN) = c66bae7704b2fa305f848451cf35b7a0738a3fd57468da1393684328f111cd75
XSIZE (dotter-20021204/dotter.LIN) = 4804333
END-of-dotter/distinfo
echo x - dotter/pkg-descr
sed 's/^X//' >dotter/pkg-descr << 'END-of-dotter/pkg-descr'
XDotter is a graphical dotplot program for detailed comparison of two sequences.
XHere, every residue in one sequence is compared to every residue in the other
Xsequence. The first sequence runs along the x-axis and the second sequence
Xalong the y-axis. In regions where the two sequences are similar to each other,
Xa row of high scores will run diagonally across the dot matrix. If you're
Xcomparing a sequence against itself to find internal repeats, you'll notice
Xthat the main diagonal scores maximally, since it's the 100% perfect
Xself-match.
X
XTo make the score matrix more intelligible, the pairwise scores are averaged
Xover a sliding window which runs diagonally. The averaged score matrix forms a
Xthree-dimensional landscape, with the two sequences in two dimensions and the
Xheight of the peaks in the third. This landscape is projected onto two
Xdimensions by aid of greyscales - the darker grey of a peak, the higher it is.
X
XDotter provides a tool to explore the visual appearance of this landscape, as
Xwell as a tool to examine the sequence alignment it represents.
X
XWWW: http://www.cgb.ki.se/cgb/groups/sonnhammer/Dotter.html
END-of-dotter/pkg-descr
exit
--- dotter.shar ends here ---

>Release-Note:
>Audit-Trail:
>Unformatted: