ports/93059: [ new port ] biology/mafft

[Fernan Aguero]

>Number:         93059
>Category:       ports
>Synopsis:       [ new port ] biology/mafft
>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 19:30:12 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:

	



--- mafft.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:
#
#	mafft
#	mafft/Makefile
#	mafft/distinfo
#	mafft/pkg-descr
#	mafft/files
#	mafft/files/patch-Makefile
#	mafft/pkg-plist
#
echo c - mafft
mkdir -p mafft > /dev/null 2>&1
echo x - mafft/Makefile
sed 's/^X//' >mafft/Makefile << 'END-of-mafft/Makefile'
X# ex:ts=8
X# New ports collection makefile for:	mafft
X# Date created:				1 Feb 2006
X# Whom:					Fernan Aguero <fernan at iib.unsam.edu.ar>
X#
X# $FreeBSD$
X#
X
XPORTNAME=	mafft
XPORTVERSION=	5.734
XCATEGORIES=	biology
XMASTER_SITES=	http://www.biophys.kyoto-u.ac.jp/~katoh/programs/align/mafft/
XDISTNAME=	${PORTNAME}-${PORTVERSION}-src
XEXTRACT_SUFX=	.tgz
X
XMAINTAINER=	fernan at iib.unsam.edu.ar
XCOMMENT=	Multiple sequence alignments based on fast Fourier transform
X
XWRKSRC=		${WRKDIR}/${PORTNAME}-${PORTVERSION}
XBUILD_WRKSRC=	${WRKSRC}/src
X
XRUN_DEPENDS=	fasta34:${PORTSDIR}/biology/fasta3
X
Xdo-install:
X	${INSTALL_SCRIPT} ${WRKSRC}/scripts/mafft ${PREFIX}/bin
X	${INSTALL_PROGRAM} ${WRKSRC}/binaries/* ${PREFIX}/bin
X	@ ${MKDIR} ${EXAMPLESDIR}
X	${INSTALL_DATA} ${WRKSRC}/test/* ${EXAMPLESDIR}
X.if !defined(NOPORTDOCS)
X	@ ${MKDIR} ${DOCSDIR}
X	${INSTALL_DATA} ${WRKSRC}/readme ${DOCSDIR}
X.endif
X
X.include <bsd.port.mk>
END-of-mafft/Makefile
echo x - mafft/distinfo
sed 's/^X//' >mafft/distinfo << 'END-of-mafft/distinfo'
XMD5 (mafft-5.734-src.tgz) = 2186ffb447554163705b841c3913f2b6
XSHA256 (mafft-5.734-src.tgz) = 2bf8e274f0200a0fb78a4aa61d800699da2071f0d3cb87701c37b33f3b038168
XSIZE (mafft-5.734-src.tgz) = 439184
END-of-mafft/distinfo
echo x - mafft/pkg-descr
sed 's/^X//' >mafft/pkg-descr << 'END-of-mafft/pkg-descr'
XMAFFT offers a range of multiple alignment strategies, L-INS-i
X(accurate; recommended for <200 sequences), FFT-NS-i (standard speed and
Xaccuracy), FFT-NS-2 (fast; recommended for >2,000 sequences), etc.
XAccording to BAliBASE and other benchmark tests, L-INS-i is one of the
Xmost accurate methods currently available.
X
XMAFFT has been described:
XK. Katoh, K. Misawa, K. Kuma and T. Miyata (Nucleic Acids Res. 30:
X3059-3066, 2002) MAFFT: a novel method for rapid multiple sequence
Xalignment based on fast Fourier transform. 
X
XWWW: http://www.biophys.kyoto-u.ac.jp/~katoh/programs/align/mafft/
END-of-mafft/pkg-descr
echo c - mafft/files
mkdir -p mafft/files > /dev/null 2>&1
echo x - mafft/files/patch-Makefile
sed 's/^X//' >mafft/files/patch-Makefile << 'END-of-mafft/files/patch-Makefile'
X--- src/Makefile.orig	Wed Aug 31 06:58:17 2005
X+++ src/Makefile	Sun Feb  5 01:07:37 2006
X@@ -1,8 +1,7 @@
X-PREFIX = \/usr\/local\/lib\/mafft
X #CC = gcc  -O2  -g -pg -static
X #CC = gcc    -mno-cygwin -O3
X #CC = gcc -O3   -mcpu=970 -mtune=970 -mpowerpc64 -mpowerpc-gpopt -falign-loops=16 -falign-functions=16 -falign-labels=16 -falign-jumps=16
X-CC = gcc -O3 
X+#CC = gcc -O3 
X #CC = gcc  -g -O0 
X PROGS = dvtditr dndfast7 dndblast sextet5 pairalign pairlocalalign \
X         disttbfast tbfast tbfast2 mafft-profile f2cl \
X@@ -71,19 +70,19 @@
X 	@echo done.
X 
X fftns: fftns.tmpl
X-	sed "s/_PREFIX/$(PREFIX)/" fftns.tmpl  > fftns
X+	sed "s,_PREFIX,$(PREFIX)," fftns.tmpl  > fftns
X fftnsi: fftnsi.tmpl
X-	sed "s/_PREFIX/$(PREFIX)/" fftnsi.tmpl > fftnsi
X+	sed "s,_PREFIX,$(PREFIX)," fftnsi.tmpl > fftnsi
X fftnsrough: fftnsrough.tmpl
X-	sed "s/_PREFIX/$(PREFIX)/" fftnsrough.tmpl  > fftnsrough
X+	sed "s,_PREFIX,$(PREFIX)," fftnsrough.tmpl  > fftnsrough
X nwns: nwns.tmpl
X-	sed "s/_PREFIX/$(PREFIX)/" nwns.tmpl   > nwns
X+	sed "s,_PREFIX,$(PREFIX)," nwns.tmpl   > nwns
X nwnsi: nwnsi.tmpl
X-	sed "s/_PREFIX/$(PREFIX)/" nwnsi.tmpl  > nwnsi
X+	sed "s,_PREFIX,$(PREFIX)," nwnsi.tmpl  > nwnsi
X nwnsrough: nwnsrough.tmpl
X-	sed "s/_PREFIX/$(PREFIX)/" nwnsrough.tmpl  > nwnsrough
X+	sed "s,_PREFIX,$(PREFIX)," nwnsrough.tmpl  > nwnsrough
X mafft: mafft.tmpl
X-	sed "s/_PREFIX/$(PREFIX)/" mafft.tmpl  > mafft
X+	sed "s,_PREFIX,$(PREFIX)," mafft.tmpl  > mafft
X 
X mltaln.h : functions.h
X 	touch mltaln.h
END-of-mafft/files/patch-Makefile
echo x - mafft/pkg-plist
sed 's/^X//' >mafft/pkg-plist << 'END-of-mafft/pkg-plist'
Xbin/mafft
Xbin/disttbfast
Xbin/dndblast
Xbin/dndfast7
Xbin/dndpre
Xbin/dndpre2
Xbin/dvtditr
Xbin/f2cl
Xbin/getlag
Xbin/mafft-profile
Xbin/pairalign
Xbin/pairlocalalign
Xbin/score
Xbin/setcore
Xbin/sextet5
Xbin/splitseq
Xbin/tbfast
Xbin/tbfast2
X%%PORTDOCS%%%%DOCSDIR%%/readme
X%%EXAMPLESDIR%%/sample
X%%EXAMPLESDIR%%/sample.fftns2
X%%EXAMPLESDIR%%/sample.fftnsi
X%%EXAMPLESDIR%%/sample.gins1
X%%EXAMPLESDIR%%/sample.ginsi
X%%EXAMPLESDIR%%/sample.lins1
X%%EXAMPLESDIR%%/sample.linsi
X%%PORTDOCS%%@dirrm %%DOCSDIR%%
X at dirrm %%EXAMPLESDIR%%
END-of-mafft/pkg-plist
exit
--- mafft.shar ends here ---

>Release-Note:
>Audit-Trail:
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