head	1.20;
access;
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	RELEASE_8_3_0:1.16
	RELEASE_9_0_0:1.16
	RELEASE_7_4_0:1.16
	RELEASE_8_2_0:1.16
	RELEASE_6_EOL:1.16
	RELEASE_8_1_0:1.16
	RELEASE_7_3_0:1.16
	RELEASE_8_0_0:1.16
	RELEASE_7_2_0:1.16
	RELEASE_7_1_0:1.16
	RELEASE_6_4_0:1.16
	RELEASE_5_EOL:1.15
	RELEASE_7_0_0:1.14
	RELEASE_6_3_0:1.14
	PRE_XORG_7:1.14
	RELEASE_4_EOL:1.12
	RELEASE_6_2_0:1.11
	RELEASE_6_1_0:1.11
	RELEASE_5_5_0:1.11
	RELEASE_6_0_0:1.6
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	RELEASE_4_11_0:1.6
	RELEASE_5_3_0:1.4
	RELEASE_4_10_0:1.4
	RELEASE_5_2_1:1.3
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	RELEASE_5_1_0:1.2
	RELEASE_4_8_0:1.2
	RELEASE_5_0_0:1.1
	RELEASE_4_7_0:1.1
	RELEASE_4_6_2:1.1
	RELEASE_4_6_1:1.1
	RELEASE_4_6_0:1.1
	RELEASE_5_0_DP1:1.1;
locks; strict;
comment	@# @;


1.20
date	2013.01.14.08.41.31;	author svnexp;	state Exp;
branches;
next	1.19;

1.19
date	2012.11.17.05.54.53;	author svnexp;	state Exp;
branches;
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1.18
date	2012.10.01.14.45.16;	author tabthorpe;	state Exp;
branches;
next	1.17;

1.17
date	2012.06.10.18.41.15;	author swills;	state Exp;
branches;
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1.16
date	2008.09.09.13.43.15;	author gahr;	state Exp;
branches;
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1.15
date	2008.04.05.10.47.11;	author rafan;	state Exp;
branches;
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1.14
date	2007.05.02.07.15.46;	author edwin;	state Exp;
branches;
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1.13
date	2007.03.09.11.26.16;	author miwi;	state Exp;
branches;
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1.12
date	2007.01.22.23.22.53;	author rafan;	state Exp;
branches;
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1.11
date	2006.02.10.09.45.28;	author lawrance;	state Exp;
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1.10
date	2005.12.06.15.10.08;	author tdb;	state Exp;
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1.9
date	2005.10.28.06.32.18;	author kris;	state Exp;
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1.8
date	2005.10.11.20.47.02;	author sem;	state Exp;
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1.7
date	2005.10.11.20.44.38;	author sem;	state Exp;
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1.6
date	2004.11.25.23.03.54;	author sem;	state Exp;
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1.5
date	2004.11.20.08.09.45;	author linimon;	state Exp;
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1.4
date	2004.01.22.12.18.01;	author trevor;	state Exp;
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1.3
date	2003.11.13.14.44.58;	author trevor;	state Exp;
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1.2
date	2003.03.07.05.56.43;	author ade;	state Exp;
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next	1.1;

1.1
date	2002.01.25.14.58.14;	author wjv;	state Exp;
branches;
next	;


desc
@@


1.20
log
@## SVN ## Exported commit - http://svnweb.freebsd.org/changeset/base/310361
## SVN ## CVS IS DEPRECATED: http://wiki.freebsd.org/CvsIsDeprecated
@
text
@# Created by: Johann Visagie <wjv@@FreeBSD.org>
# $FreeBSD: head/biology/t_coffee/Makefile 310361 2013-01-14 08:04:38Z araujo $

PORTNAME=	t_coffee
PORTVERSION=	9.03
DISTVERSIONSUFFIX=	.r1318
CATEGORIES=	biology
MASTER_SITES=	http://www.tcoffee.org/Packages/Stable/%SUBDIR%/
MASTER_SITE_SUBDIR=	Version_${PORTVERSION}${DISTVERSIONSUFFIX}
DISTNAME=	T-COFFEE_distribution_Version_${PORTVERSION}${DISTVERSIONSUFFIX}

MAINTAINER=	ports@@FreeBSD.org
COMMENT=	A multiple DNA or protein sequence alignment package

LICENSE=	GPLv2

RUN_DEPENDS=	clustalw:${PORTSDIR}/biology/clustalw

OPTIONS_DEFINE=	EXAMPLES

BUILD_WRKSRC=	${WRKSRC}/t_coffee_source

USE_FORTRAN=	yes
MAKE_ENV=	FCC="${FC} ${FFLAGS}"
MAKEFILE=	makefile
MAKE_JOBS_SAFE=	yes

PORTEXAMPLES=	*
PLIST_FILES=	bin/TMalign bin/t_coffee

.include <bsd.port.options.mk>

do-install:
	(cd ${BUILD_WRKSRC} \
		&& ${INSTALL_PROGRAM} TMalign t_coffee ${PREFIX}/bin)
.if ${PORT_OPTIONS:MEXAMPLES}
	@@${MKDIR} ${EXAMPLESDIR}
	@@(cd ${WRKSRC}/example && ${COPYTREE_SHARE} . ${EXAMPLESDIR})
.endif

.include <bsd.port.mk>
@


1.19
log
@Switch exporter over
@
text
@d2 1
a2 1
# $FreeBSD: head/biology/t_coffee/Makefile 305130 2012-10-01 14:45:16Z tabthorpe $
d5 2
a6 1
PORTVERSION=	5.68
d8 3
a10 2
MASTER_SITES=	http://www.tcoffee.org/Packages/
DISTNAME=	T-COFFEE_distribution_Version_${PORTVERSION}
d15 5
a19 2
BUILD_DEPENDS=	clustalw:${PORTSDIR}/biology/clustalw
RUN_DEPENDS:=	${BUILD_DEPENDS}
a21 2
MAKE_ENV=	MV=${MV} USER_BIN=${PREFIX}/bin \
		CLUSTALW_4_TCOFFEE=${LOCALBASE}/bin/clustalw
d23 2
d26 6
d34 5
a38 12
	${INSTALL_PROGRAM} ${WRKSRC}/bin/t_coffee ${PREFIX}/bin

post-install:
.if !defined(NOPORTDOCS)
	@@ ${MKDIR} ${DOCSDIR}/html
	${INSTALL_DATA} ${WRKSRC}/doc/* ${DOCSDIR}
	${INSTALL_DATA} ${WRKSRC}/license.txt ${DOCSDIR}
	${INSTALL_DATA} ${WRKSRC}/html/* ${DOCSDIR}/html
.endif
.if !defined(NOPORTEXAMPLES)
	@@ ${MKDIR} ${EXAMPLESDIR}
	cd ${WRKSRC}/example && ${COPYTREE_SHARE} \* ${EXAMPLESDIR}
@


1.18
log
@SVN rev 305130 on 2012-10-01 14:45:16Z by tabthorpe

- Reassign to the heap at maintainer's request
@
text
@d2 1
a2 1
# $FreeBSD$
@


1.17
log
@- Convert all remaining instances of BUILD_DEPENDS=${RUN_DEPENDS} or
  RUN_DEPENDS=${BUILD_DEPENDS} to use := which portlint has warned
  about for a while.

PR:		ports/168208
Approved by:	portmgr (miwi)
@
text
@d1 1
a1 5
# ex:ts=8
# New ports collection makefile for:	t_coffee
# Date created:		27 June 2001
# Whom:	      		Johann Visagie <wjv@@FreeBSD.org>
#
a2 1
#
d10 1
a10 1
MAINTAINER=	fernan@@iib.unsam.edu.ar
@


1.16
log
@- Respect PORTDOCS/PORTEXAMPLES

Reported by:	QA Tindie
Approved by:	portmgr
@
text
@d19 1
a19 1
RUN_DEPENDS=	${BUILD_DEPENDS}
@


1.15
log
@- Update to 5.68
- Remove gcc version restriction

PR:		ports/122435
Submitted by:	Fernan Aguero <fernan at iib.unsam.edu.ar> (maintainer)
@
text
@d32 1
a32 1
	@@ ${MKDIR} ${DOCSDIR}
d34 4
d39 1
a39 6
	@@ cd ${WRKSRC}/example && ${FIND} * \
	  | ${CPIO} --quiet -pdum -R ${SHAREOWN}:${SHAREGRP} ${EXAMPLESDIR}
	@@ ${MKDIR} ${DATADIR}
	${INSTALL_DATA} ${WRKSRC}/license.txt ${DATADIR}
	@@ ${MKDIR} ${DATADIR}/html
	${INSTALL_DATA} ${WRKSRC}/html/* ${DATADIR}/html
@


1.14
log
@[patch] cleanup non-supported FreeBSD versions

PR:		ports/111728
Submitted by:	Edwin Groothuis <edwin@@mavetju.org>
Approved by:	maintainer timeout
@
text
@d10 1
a10 1
PORTVERSION=	4.96
a25 1
USE_GCC=	3.3
@


1.13
log
@- Update to 4.96

PR:             110080
Submitted by:   Fernan Aguero<fernan@@iib.unsam.edu.ar> (maintainer)
@
text
@d26 1
d44 1
a44 7
.include <bsd.port.pre.mk>

.if ${OSVERSION} > 502126
USE_GCC=3.3
.endif

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


1.12
log
@- Project moves to a new home. Change MASTER_SITES and WWW

PR:		ports/108214
Submitted by:	Thomas Abthorpe <thomas at goodking.ca>
Approved by:	Fernan Aguero <fernan at iib.unsam.edu.ar> (maintainer)
@
text
@d10 1
a10 1
PORTVERSION=	3.27
@


1.11
log
@Update to 3.27.
Use GCC 3.3 on systems with 3.4, due to an internal compiler error.

PR:		ports/93050
Submitted by:	Fernan Aguero <fernan@@iib.unsam.edu.ar> (maintainer)
@
text
@d12 1
a12 1
MASTER_SITES=	http://igs-server.cnrs-mrs.fr/~cnotred/Packages/
@


1.10
log
@- Update to 3.18 to make fetchable again
- Mark broken on 6.x upwards

PR:		89977
Submitted by:	Fernan Aguero <fernan@@iib.unsam.edu.ar> (maintainer)
Approved by:	clement (mentor)
@
text
@d10 1
a10 1
PORTVERSION=	3.18
d28 1
a28 1
	@@ ${INSTALL_PROGRAM} ${WRKSRC}/bin/t_coffee ${PREFIX}/bin
d33 1
a33 1
	@@ ${INSTALL_DATA} ${WRKSRC}/doc/* ${DOCSDIR}
d38 1
a38 1
	@@ ${INSTALL_DATA} ${WRKSRC}/license.txt ${DATADIR}
d40 1
a40 1
	@@ ${INSTALL_DATA} ${WRKSRC}/html/* ${DATADIR}/html
d45 2
a46 2
.if ${OSVERSION} >= 600000
BROKEN=		"Does not build on FreeBSD >= 6.x"
@


1.9
log
@BROKEN: Unfetchable
@
text
@d10 1
a10 1
PORTVERSION=	3.14
a20 2
BROKEN=		Unfetchable

d43 7
a49 1
.include <bsd.port.mk>
@


1.8
log
@Forced commit to note the port was updated to 3.14 not 3.13
@
text
@d21 2
@


1.7
log
@- Update to 3.13. It fixes fetching.

PR:		ports/87264
Submitted by:	maintainer
@
text
@@


1.6
log
@- Update to 2.03
- Pass maintainership to submitter

PR:		ports/74332
Submitted by:	Fernan Aguero <fernan(at)iib.unsam.edu.ar>
@
text
@d1 1
d10 1
a10 1
PORTVERSION=	2.03
a25 3
SCRIPTS=	msf_aln2fasta_aln.pl blast_aln2fasta_aln.pl \
		fasta_aln2fasta_aln_unique_name.pl extract_from_pdb \
		fugue_client t_coffee_dpa t_coffee_dpa2 mocca
a28 3
.for scriptfile in ${SCRIPTS}
	@@ ${INSTALL_SCRIPT} ${WRKSRC}/bin/${scriptfile} ${PREFIX}/bin
.endfor
a34 1
	@@ ${RMDIR} ${WRKSRC}/example/aln 2>/dev/null || ${TRUE}
d37 4
@


1.5
log
@With portmgr hat on, reset inactive maintainer.  These ports are now up
for adoption.
@
text
@d9 1
a9 1
PORTVERSION=	1.37
d12 1
a12 1
DISTNAME=	T-COFFEE_distribution
d14 1
a14 1
MAINTAINER=	ports@@FreeBSD.org
a19 1
WRKSRC=		${WRKDIR}/${DISTNAME}_Version_${PORTVERSION}
d21 3
a23 2
MAKE_ENV=	MV=${MV} USER_BIN=${LOCALBASE}/bin \
	  	CLUSTALW_4_TCOFFEE=${LOCALBASE}/bin/clustalw
d25 3
a27 7
PKGMESSAGE=	${WRKDIR}/pkg-message

post-build:
	@@ cd ${WRKSRC}/lalign && ${SETENV} ${MAKE_ENV} ${MAKE} \
	  ${MAKE_FLAGS} ${MAKEFILE} ${MAKE_ARGS} ${ALL_TARGET}

.include <bsd.port.pre.mk>
d30 2
a31 4
.for binfile in t_coffee_source/t_coffee lalign/lalign2list
	@@ ${INSTALL_PROGRAM} ${WRKSRC}/${binfile} ${PREFIX}/bin
.endfor
.for scriptfile in extract_from_pdb mocca
a35 2
	@@ ${MKDIR} ${DATADIR}
	@@ ${INSTALL_DATA} ${WRKSRC}/html/* ${DATADIR}
a42 4
	@@ ${SED} -e 's#%%DATADIR%%#${DATADIR}#' ${.CURDIR}/pkg-message \
	  > ${PKGMESSAGE}
.if !defined(BATCH)
	@@ ${CAT} ${PKGMESSAGE}
d44 2
a45 2
.endif
.include <bsd.port.post.mk>
@


1.4
log
@Use the CPIO macro defined in bsd.port.mk.
@
text
@d14 1
a14 1
MAINTAINER=	wjv@@FreeBSD.org
@


1.3
log
@Use the FIND and XARGS macros introduced in bsd.port.mk 1.391.
@
text
@d50 1
a50 1
	  | cpio --quiet -pdum -R ${SHAREOWN}:${SHAREGRP} ${EXAMPLESDIR}
@


1.2
log
@Clear moonlight beckons.
Requiem mors pacem pkg-comment,
And be calm ports tree.

E Nomini Patri, E Fili, E Spiritu Sancti.
@
text
@d49 1
a49 1
	@@ cd ${WRKSRC}/example && find * \
@


1.1
log
@Add t_coffee 1.37, a multiple DNA or protein sequence alignment package.
@
text
@d15 1
@

