head	1.6;
access;
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	RELEASE_7_4_0:1.3
	RELEASE_8_2_0:1.3
	RELEASE_6_EOL:1.2
	RELEASE_8_1_0:1.1
	RELEASE_7_3_0:1.1
	RELEASE_8_0_0:1.1;
locks; strict;
comment	@# @;


1.6
date	2013.02.04.13.32.33;	author svnexp;	state Exp;
branches;
next	1.5;

1.5
date	2012.12.04.21.06.14;	author svnexp;	state Exp;
branches;
next	1.4;

1.4
date	2012.11.17.05.54.52;	author svnexp;	state Exp;
branches;
next	1.3;

1.3
date	2010.12.04.07.30.35;	author ade;	state Exp;
branches;
next	1.2;

1.2
date	2010.10.05.19.57.26;	author ade;	state Exp;
branches;
next	1.1;

1.1
date	2009.07.21.01.10.13;	author amdmi3;	state Exp;
branches;
next	;


desc
@@


1.6
log
@## SVN ## Exported commit - http://svnweb.freebsd.org/changeset/base/311601
## SVN ## CVS IS DEPRECATED: http://wiki.freebsd.org/CvsIsDeprecated
@
text
@# Created by: ballen
# $FreeBSD: head/biology/phyml/Makefile 311601 2013-02-04 10:07:30Z araujo $

PORTNAME=	phyml
PORTVERSION=	20121109
CATEGORIES=	biology
MASTER_SITES=	GOOGLE_CODE
DISTNAME=	${PORTNAME}-20120412
DIST_SUBDIR=	${PORTNAME}

PATCH_SITES=	${MASTER_SITES}
PATCHFILES=	${PORTVERSION}.patch
PATCH_DIST_STRIP=	-p4

MAINTAINER=	ports@@FreeBSD.org
COMMENT=	Simple, fast, and accurate algorithm to estimate large phylogenies

LICENSE=	GPLv2

PATCH_WRKSRC=	${WRKSRC}/src

USE_AUTOTOOLS=	aclocal autoheader automake autoconf
AUTOMAKE_ARGS=	--add-missing
MAKE_JOBS_SAFE=	yes

PLIST_FILES=	bin/phyml

post-patch:
	@@${REINPLACE_CMD} -e \
		'/^AC_INIT/s|,esyscmd.*,|,[${PORTVERSION}],| ; \
		 s|-O2 -msse|$${CFLAGS}|' ${WRKSRC}/configure.ac

.include <bsd.port.mk>
@


1.5
log
@## SVN ## Exported commit - http://svnweb.freebsd.org/changeset/base/308268
## SVN ## CVS IS DEPRECATED: http://wiki.freebsd.org/CvsIsDeprecated
## SVN ##
## SVN ## ------------------------------------------------------------------------
## SVN ## r308268 | zi | 2012-12-04 20:28:16 +0000 (Tue, 04 Dec 2012) | 5 lines
## SVN ##
## SVN ## - Reset MAINTAINER due to unrecoverable email bounce
## SVN ##
## SVN ## Reported by:	portscout
## SVN ## Feature safe:	yes
## SVN ##
## SVN ## ------------------------------------------------------------------------
## SVN ##
@
text
@d1 2
a2 6
# New ports collection makefile for:   phyml 3.0 20090706
# Date created:        July 17, 2009
# Whom:                ballen
#
# $FreeBSD: head/biology/phyml/Makefile 308268 2012-12-04 20:28:16Z zi $
#
d5 1
a5 1
PORTVERSION=	20090706
d8 6
a13 1
DISTNAME=	phyml_20090706
d16 5
a20 1
COMMENT=	A simple, fast, and accurate algorithm to estimate large phylogenies
d22 1
a22 4
WRKSRC=		${WRKDIR}/${PORTNAME}/src
GNU_CONFIGURE=	yes
PLIST_FILES=	bin/phyml
USE_AUTOTOOLS=	automake aclocal
d24 1
d26 1
a26 4
.include <bsd.port.pre.mk>

pre-configure:
	${RM} ${WRKSRC}/missing
d28 4
a31 2
pre-install:
	${CHMOD} a+x ${WRKSRC}/install-sh
d33 1
a33 1
.include <bsd.port.post.mk>
@


1.4
log
@Switch exporter over
@
text
@d5 1
a5 1
# $FreeBSD: head/biology/phyml/Makefile 300895 2012-07-14 12:56:14Z beat $
d14 1
a14 1
MAINTAINER=	ben@@sysadminschronicles.com
@


1.3
log
@Sync to new bsd.autotools.mk
@
text
@d5 1
a5 1
# $FreeBSD$
@


1.2
log
@Round one migration of ports from automake{19,110} to automake111
@
text
@d20 1
a20 1
USE_AUTOTOOLS=	automake:111 aclocal:111
@


1.1
log
@PhyML is a software that estimates maximum likelihood phylogenies from
alignments of nucleotide or amino acid sequences. It provides a wide range of
options that were designed to facilitate standard phylogenetic analyses. The
main strengths of PhyML lies in the large number of substitution models coupled
to various options to search the space of phylogenetic tree topologies, going
from very fast and efficient methods to slower but generally more accurate
approaches. It also implements two methods to evaluate branch supports in a
sound statistical framework (the non-parametric bootstrap and the approximate
likelihood ratio test). PhyML was designed to process moderate to large data
sets. In theory, alignments with up to 4,000 sequences 2,000,000 character-long
can analyzed. In practice however, the amount of memory required to process a
data set is proportional of the product of the number of sequences by their
length. Hence, a large number of sequences can only be processed provided that
they are short. Also, PhyML can handle long sequences provided that they are
not numerous. With most standard personal computers, the "comfort zone" for
PhyML generally lies around 3 to 500 sequences less than 2,000 character long.

WWW: http://code.google.com/p/phyml/

PR:		136877
Submitted by:	Ben Allen <ben@@sysadminschronicles.com>
@
text
@d20 1
a20 1
USE_AUTOTOOLS=	automake:110 aclocal:110
@

