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1.5
date	2012.11.17.05.54.52;	author svnexp;	state Exp;
branches;
next	1.4;

1.4
date	2012.07.24.07.19.21;	author cs;	state Exp;
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1.3
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1.1
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desc
@@


1.5
log
@Switch exporter over
@
text
@# New ports collection makefile for:	muscle
# Date created:	6 December 2007
# Whom:		Motomichi Matsuzaki <mzaki@@biol.s.u-tokyo.ac.jp>
#
# $FreeBSD: head/biology/muscle/Makefile 301441 2012-07-24 07:19:21Z cs $
#

PORTNAME=	muscle
PORTVERSION=	3.6
CATEGORIES=	biology
MASTER_SITES=	http://www.drive5.com/muscle/downloads${PORTVERSION}/
DISTNAME=	${PORTNAME}${PORTVERSION}_src

.if !defined(NOPORTDOCS)
EXTRACT_ONLY=	${DISTNAME}${EXTRACT_SUFX}
DISTFILES=	${EXTRACT_ONLY}
PORTDOCS=	${PORTNAME}.pdf ${PORTNAME}.html
MASTER_SITES+=	http://www.drive5.com/muscle/:docs
.for file in ${PORTDOCS}
DISTFILES+=	${file}:docs
.endfor
.endif

MAINTAINER=	mzaki@@m.u-tokyo.ac.jp
COMMENT=	Multiple Sequence Comparison by Log-Expectation

FETCH_ARGS=	-A

USE_GMAKE=	yes
USE_DOS2UNIX=	*.cpp

PLIST_FILES=	bin/muscle

do-install:
	${INSTALL_PROGRAM} ${WRKSRC}/muscle ${PREFIX}/bin
.if !defined(NOPORTDOCS)
	@@${MKDIR} ${DOCSDIR}
.for file in ${PORTDOCS}
	@@${INSTALL_DATA} ${DISTDIR}/${file} ${DOCSDIR}
.endfor
.endif

.include <bsd.port.mk>
@


1.4
log
@SVN rev 301441 on 2012-07-24 07:19:21Z by cs

Fix typos in COMMENT
@
text
@d5 1
a5 1
# $FreeBSD$
@


1.3
log
@- Update maintainer's email address

Submitted by:	Motomichi Matsuzaki <mzaki@@m.u-tokyo.ac.jp> (maintainer)
@
text
@d25 1
a25 1
COMMENT=	MUltiple Sequence Comparison by Log-Expectation
@


1.2
log
@- Try to fix fetch

Submitted by:	Motomichi Matsuzaki <mzaki@@m.u-tokyo.ac.jp> (maintainer)
@
text
@d24 1
a24 1
MAINTAINER=	mzaki@@biol.s.u-tokyo.ac.jp
@


1.1
log
@MUSCLE is multiple alignment software for protein and nucleotide sequences.
The name stands for multiple sequence comparison by log-expectation.

A range of options is provided that give you the choice of optimizing
accuracy, speed, or some compromise between the two. Default parameters are
those that give the best average accuracy in the published tests. MUSCLE
can achieve both better average accuracy and better speed than CLUSTALW or
T-Coffee, depending on the chosen options.

Citation:

Edgar, R. C. (2004) MUSCLE: multiple sequence alignment with high accuracy
and high throughput. Nucleic Acids Research 32(5): 1792-1797.

Edgar, R. C. (2004) MUSCLE: a multiple sequence alignment method with
reduced time and space complexity. BMC Bioinformatics 5(1): 113.

The NAR paper gives only a brief overview of the algorithm and
implementation details. For a full discussion of the method and many of
the non-default options that it offers, please see the BMC paper.

WWW: http://www.drive5.com/muscle/

PR:		ports/118460
Submitted by:	Motomichi Matsuzaki <mzaki@@biol.s.u-tokyo.ac.jp>
@
text
@d27 2
@

