head	1.9;
access;
symbols
	RELEASE_8_3_0:1.5
	RELEASE_9_0_0:1.5
	RELEASE_7_4_0:1.5
	RELEASE_8_2_0:1.5
	RELEASE_6_EOL:1.4
	RELEASE_8_1_0:1.4
	RELEASE_7_3_0:1.4
	RELEASE_8_0_0:1.4
	RELEASE_7_2_0:1.4
	RELEASE_7_1_0:1.3
	RELEASE_6_4_0:1.3
	RELEASE_5_EOL:1.3
	RELEASE_7_0_0:1.2
	RELEASE_6_3_0:1.2
	PRE_XORG_7:1.2
	RELEASE_4_EOL:1.2
	RELEASE_6_2_0:1.2;
locks; strict;
comment	@# @;


1.9
date	2012.11.17.05.54.52;	author svnexp;	state Exp;
branches;
next	1.8;

1.8
date	2012.09.08.08.30.39;	author linimon;	state Exp;
branches;
next	1.7;

1.7
date	2012.08.07.13.54.02;	author scheidell;	state Exp;
branches;
next	1.6;

1.6
date	2012.08.07.12.26.39;	author scheidell;	state Exp;
branches;
next	1.5;

1.5
date	2011.01.27.17.26.45;	author pav;	state Exp;
branches;
next	1.4;

1.4
date	2009.02.04.03.31.00;	author pgollucci;	state Exp;
branches;
next	1.3;

1.3
date	2008.04.01.22.24.51;	author pav;	state Exp;
branches;
next	1.2;

1.2
date	2006.03.19.12.59.16;	author garga;	state Exp;
branches;
next	1.1;

1.1
date	2006.03.15.10.41.16;	author garga;	state Exp;
branches;
next	;


desc
@@


1.9
log
@Switch exporter over
@
text
@# ex:ts=8
# New ports collection makefile for:	mafft
# Date created:				1 Feb 2006
# Whom:					Fernan Aguero <fernan@@iib.unsam.edu.ar>
#
# $FreeBSD: head/biology/mafft/Makefile 303880 2012-09-08 08:30:39Z linimon $
#

PORTNAME=	mafft
PORTVERSION=	6.903
CATEGORIES=	biology
MASTER_SITES=	http://mafft.cbrc.jp/alignment/software/
DISTNAME=	${PORTNAME}-${PORTVERSION}-without-extensions-src
EXTRACT_SUFX=	.tgz

MAINTAINER=	cartwright@@asu.edu
COMMENT=	Multiple alignment program for amino acid or nucleotide sequences

LICENSE=	BSD

RUN_DEPENDS=	lav2ps:${PORTSDIR}/biology/fasta3

WRKSRC=		${WRKDIR}/${PORTNAME}-${PORTVERSION}-without-extensions
BUILD_WRKSRC=	${WRKSRC}/core

USE_GMAKE=	yes

MAN1=		mafft.1 mafft-homologs.1

LIBEXEC_FILES=	dvtditr dndfast7 dndblast sextet5 mafft-distance pairlocalalign \
		pair2hat3s multi2hat3s rnatest pairash addsingle splittbfast \
		disttbfast tbfast mafft-profile f2cl mccaskillwrap contrafoldwrap \
		countlen seq2regtable regtable2seq score getlag dndpre dndpre2 \
		setcore replaceu restoreu setdirection makedirectionlist version
SCRIPT_FILES=	mafft mafft-homologs.rb
LN_FILES=	einsi fftns fftnsi ginsi linsi mafft-einsi mafft-fftns \
		mafft-fftnsi mafft-ginsi mafft-linsi mafft-nwns mafft-nwnsi \
		mafft-qinsi mafft-xinsi nwns nwnsi

.include <bsd.port.pre.mk>

.if ${ARCH} == "sparc64"
BROKEN=		Does not install on sparc64: depends on thread-local storage
.endif

post-patch:
	@@${REINPLACE_CMD} -e 's|-lpthread|${PTHREAD_LIBS}|' \
	                  -e 's|^MANDIR = .*$$|MANDIR = $$(MANPREFIX)/man/man1|' \
	                  -e 's|^PREFIX = .*$$||' \
	                  -e 's|^CC = .*$$||' \
	                  -e 's|^CFLAGS = .*$$||' \
		${BUILD_WRKSRC}/Makefile

do-install:
	@@${MKDIR} ${PREFIX}/libexec/${PORTNAME}
.for exec in ${LIBEXEC_FILES}
	${INSTALL_PROGRAM} ${WRKSRC}/binaries/${exec} ${PREFIX}/libexec/${PORTNAME}
.endfor
.for exec in ${SCRIPT_FILES}
	${INSTALL_SCRIPT} ${WRKSRC}/scripts/${exec} ${PREFIX}/bin
.endfor
.for exec in ${LN_FILES}
	${LN} -fs ${PREFIX}/bin/mafft ${PREFIX}/bin/${exec}
.endfor
	${LN} -fs ${PREFIX}/libexec/${PORTNAME}/mafft-distance ${PREFIX}/bin/mafft-distance
	${LN} -fs ${PREFIX}/libexec/${PORTNAME}/mafft-profile ${PREFIX}/bin/mafft-profile
.for man in ${MAN1}
	${INSTALL_MAN} ${WRKSRC}/binaries/${man} ${MAN1PREFIX}/man/man1
.endfor
	@@${MKDIR} ${EXAMPLESDIR}
	${INSTALL_DATA} ${WRKSRC}/test/* ${EXAMPLESDIR}
.if !defined(NOPORTDOCS)
	@@${MKDIR} ${DOCSDIR}
	${INSTALL_DATA} ${WRKSRC}/readme ${DOCSDIR}
	${INSTALL_DATA} ${WRKSRC}/license ${DOCSDIR}
.endif

.include <bsd.port.post.mk>
@


1.8
log
@SVN rev 303880 on 2012-09-08 08:30:39Z by linimon

Mark as broken on sparc64: depends on thread-local storage, which is not
available on sparc64.

Hat:		portmgr
@
text
@d6 1
a6 1
# $FreeBSD$
@


1.7
log
@SVN rev 302238 on 2012-08-07 13:54:02Z by scheidell

- Submitter is now maintainer

PR:		ports/169920
Approved by:	Fernan Aguero <fernan@@iib.unsam.edu.ar> (maintainer)
@
text
@d42 4
@


1.6
log
@SVN rev 302236 on 2012-08-07 12:26:39Z by scheidell

- Update to version 6.903

PR:		ports/169920
Submitted by:	"Reed A. Cartwright" <cartwright@@asu.edu>
Approved by:	maintainer (timeout, 21 days)
@
text
@d16 1
a16 1
MAINTAINER=	fernan@@iib.unsam.edu.ar
@


1.5
log
@- Change depobj for fasta3 to something that does not change on fasta updates

Reported by:	pointyhat
Feature safe:	yes
@
text
@d10 1
a10 1
PORTVERSION=	5.743
d12 2
a13 2
MASTER_SITES=	http://align.bmr.kyushu-u.ac.jp/mafft/software/
DISTNAME=	${PORTNAME}-${PORTVERSION}-src
d17 3
a19 1
COMMENT=	Multiple sequence alignments based on fast Fourier transform
d23 16
a38 2
WRKSRC=		${WRKDIR}/${PORTNAME}-${PORTVERSION}
BUILD_WRKSRC=	${WRKSRC}/src
d40 1
a40 1
MAKE_ENV+=	CFLAG="${CFLAGS}"
d43 6
a48 2
	@@${REINPLACE_CMD} -E 's,^(CC|PREFIX) =,\1 ?=,' \
		${WRKSRC}/src/Makefile
d51 16
a66 3
	${INSTALL_SCRIPT} ${WRKSRC}/scripts/mafft ${PREFIX}/bin
	${INSTALL_PROGRAM} ${WRKSRC}/binaries/* ${PREFIX}/bin
	@@ ${MKDIR} ${EXAMPLESDIR}
d69 1
a69 1
	@@ ${MKDIR} ${DOCSDIR}
d71 1
d74 1
a74 1
.include <bsd.port.mk>
@


1.4
log
@- Update download locations, update WWW

Reported by:    -fetch-original pointyhat run
@
text
@d19 1
a19 1
RUN_DEPENDS=	fasta35:${PORTSDIR}/biology/fasta3
@


1.3
log
@- Chase fasta3 update

Reported by:	pointyhat
@
text
@d12 1
a12 2
MASTER_SITES=	http://www.biophys.kyoto-u.ac.jp/~katoh/programs/align/mafft/ \
		http://genoma.unsam.edu.ar/~fernan/freebsd/distfiles/
@


1.2
log
@- Update to 5.743
- Add a MASTER_SITE backup since oficial one just have last version and make
  it fetchable again

Submitted by:	maintainer by email
Reported by:	krismail
@
text
@d20 1
a20 1
RUN_DEPENDS=	fasta34:${PORTSDIR}/biology/fasta3
@


1.1
log
@Add mafft 5.734, multiple sequence alignments based on fast Fourier
transform.

PR:		ports/93059
Submitted by:	Fernan Aguero <fernan@@iib.unsam.edu.ar>
@
text
@d10 1
a10 1
PORTVERSION=	5.734
d12 2
a13 1
MASTER_SITES=	http://www.biophys.kyoto-u.ac.jp/~katoh/programs/align/mafft/
d27 4
@

