ports/93058: [ new port ] biology/lagan

Wed Feb 8 19:30:15 UTC 2006

>Number:         93058
>Category:       ports
>Synopsis:       [ new port ] biology/lagan
>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 19:30:08 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:
	
	
>How-To-Repeat:
	
	
>Fix:

	
--- lagan.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:
#
#	lagan
#	lagan/Makefile
#	lagan/pkg-descr
#	lagan/distinfo
#	lagan/pkg-plist
#	lagan/files
#	lagan/files/pkg-message.in
#
echo c - lagan
mkdir -p lagan > /dev/null 2>&1
echo x - lagan/Makefile
sed 's/^X//' >lagan/Makefile << 'END-of-lagan/Makefile'
X# ex:ts=8
X# New ports collection makefile for:	lagan
X# Date created:		07 Dec 2005
X# Whom:	      		Fernan Aguero <fernan at iib.unsam.edu.ar>
X#
X# $FreeBSD$
X#
X
XPORTNAME=	lagan
XPORTVERSION=	1.2
XCATEGORIES=	biology
XMASTER_SITES=	http://lagan.stanford.edu/lagan_web/
XDISTNAME=	${PORTNAME}${PORTVERSION:S/.//}
X
XMAINTAINER=	fernan at iib.unsam.edu.ar
XCOMMENT=	Efficient tools for large-scale multiple alignments of genomic DNA
X
XLAGAN_DIR=	${PREFIX}/${PORTNAME}
XUSE_PERL5_RUN=	yes
XSUB_FILES=	pkg-message
XSUB_LIST=	LAGAN_DIR=${LAGAN_DIR}
X
XEXECUTABLES=	anchors chaos glocal mlagan order
XSCRIPTS=	anal_gloc.pl lagan.pl rechaos.pl slagan.pl
XEXEUTILS=	Glue bin2bl bin2mf cextract contigorder cstat dotplot fa2xfa \
X		getbounds getcontigpos getlength getoverlap rc scorealign \
X		scorecontigs seqmerge
XSCRIPTUTILS=	cmerge2.pl draft.pl mextract.pl mf2bin.pl mpretty.pl \
X		mproject.pl mrun.pl mrunfile.pl mrunpairs.pl mviz.pl
X
Xdo-install:
X	@${MKDIR} ${LAGAN_DIR}
X	${CP} -R ${WRKSRC}/Readmes ${LAGAN_DIR}
X.for exe in ${EXECUTABLES}
X	${INSTALL_PROGRAM} ${WRKSRC}/${exe} ${LAGAN_DIR}
X.endfor
X.for script in ${SCRIPTS}
X	${INSTALL_SCRIPT} ${WRKSRC}/${script} ${LAGAN_DIR}
X.endfor
X	@${MKDIR} ${LAGAN_DIR}/utils
X.for exeutil in ${EXEUTILS}
X	${INSTALL_PROGRAM} ${WRKSRC}/utils/${exeutil} ${LAGAN_DIR}/utils
X.endfor
X.for scriptutil in ${SCRIPTUTILS}
X	${INSTALL_SCRIPT} ${WRKSRC}/utils/${scriptutil} ${LAGAN_DIR}/utils
X.endfor
X	@${CAT} ${PKGMESSAGE}
X
X.include <bsd.port.mk>
END-of-lagan/Makefile
echo x - lagan/pkg-descr
sed 's/^X//' >lagan/pkg-descr << 'END-of-lagan/pkg-descr'
XThe LAGAN Toolkit consists of four components: 
X
X CHAOS, a pairwise local aligner optimized for non-coding, and other
X poorly conserved regions of the genome.
X 
X LAGAN, a highly parametrizable pairwise global alignment using local
X alignments generated by CHAOS as anchors.
X 
X Multi-LAGAN, a progressive pairwise algorithm to produce multiple
X sequence alignments.
X 
X Shuffle-LAGAN, a novel glocal algorithm that is able to find
X rearrangements in a global alignment.
X
XFast and sensitive multiple alignment of long genomic sequences. BMC
XBioinformatics 2003 4:66.
X
XLAGAN and Multi-LAGAN: efficient tools for large-scale multiple
Xalignment of genomic DNA. Genome Res 2003 13(4): 721-31.
X
XGlocal alignment: finding rearrangements during alignment. Proceedings
Xof the ISMB 2003, Bioinformatics 19: 54i-62i.
X
XWWW: http://lagan.stanford.edu/lagan_web/
END-of-lagan/pkg-descr
echo x - lagan/distinfo
sed 's/^X//' >lagan/distinfo << 'END-of-lagan/distinfo'
XMD5 (lagan12.tar.gz) = e45c9287d04b31924115869588f1fb61
XSHA256 (lagan12.tar.gz) = d27754367b3aa9bf34976f7a619d5024be444b47cba370e3f53d0bba87389d4a
XSIZE (lagan12.tar.gz) = 112894
END-of-lagan/distinfo
echo x - lagan/pkg-plist
sed 's/^X//' >lagan/pkg-plist << 'END-of-lagan/pkg-plist'
Xlagan/Readmes/README.mlagan
Xlagan/Readmes/README.FIRST
Xlagan/Readmes/README.lagan
Xlagan/Readmes/README.chaos
Xlagan/Readmes/README.tools
Xlagan/Readmes/README.shuffle
Xlagan/Readmes/LICENSE
Xlagan/anchors
Xlagan/chaos
Xlagan/glocal
Xlagan/mlagan
Xlagan/order
Xlagan/anal_gloc.pl
Xlagan/lagan.pl
Xlagan/rechaos.pl
Xlagan/slagan.pl
Xlagan/utils/Glue
Xlagan/utils/bin2bl
Xlagan/utils/bin2mf
Xlagan/utils/cextract
Xlagan/utils/contigorder
Xlagan/utils/cstat
Xlagan/utils/dotplot
Xlagan/utils/fa2xfa
Xlagan/utils/getbounds
Xlagan/utils/getcontigpos
Xlagan/utils/getlength
Xlagan/utils/getoverlap
Xlagan/utils/rc
Xlagan/utils/scorealign
Xlagan/utils/scorecontigs
Xlagan/utils/seqmerge
Xlagan/utils/cmerge2.pl
Xlagan/utils/draft.pl
Xlagan/utils/mextract.pl
Xlagan/utils/mf2bin.pl
Xlagan/utils/mpretty.pl
Xlagan/utils/mproject.pl
Xlagan/utils/mrun.pl
Xlagan/utils/mrunfile.pl
Xlagan/utils/mrunpairs.pl
Xlagan/utils/mviz.pl
X at dirrm lagan/Readmes
X at unexec rmdir %Dlagan/utils 2>/dev/null || true
X at unexec rmdir %Dlagan 2>/dev/null || true
END-of-lagan/pkg-plist
echo c - lagan/files
mkdir -p lagan/files > /dev/null 2>&1
echo x - lagan/files/pkg-message.in
sed 's/^X//' >lagan/files/pkg-message.in << 'END-of-lagan/files/pkg-message.in'
X===============================================================================
X
X All the executables, scripts, Readmes and utilities were installed
X under %%LAGAN_DIR%%
X 
X Add this to your PATH and set the environment variable
X LAGAN_DIR to point to this directory.
X 
X===============================================================================
END-of-lagan/files/pkg-message.in
exit
--- lagan.shar ends here ---

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