head	1.6;
access;
symbols
	RELEASE_8_3_0:1.3
	RELEASE_9_0_0:1.3
	RELEASE_7_4_0:1.3
	RELEASE_8_2_0:1.3
	RELEASE_6_EOL:1.3
	RELEASE_8_1_0:1.2
	RELEASE_7_3_0:1.2
	RELEASE_8_0_0:1.2
	RELEASE_7_2_0:1.2
	RELEASE_7_1_0:1.2
	RELEASE_6_4_0:1.2
	RELEASE_5_EOL:1.1
	RELEASE_7_0_0:1.1
	RELEASE_6_3_0:1.1
	PRE_XORG_7:1.1
	RELEASE_4_EOL:1.1
	RELEASE_6_2_0:1.1;
locks; strict;
comment	@# @;


1.6
date	2012.11.17.22.22.43;	author svnexp;	state Exp;
branches;
next	1.5;

1.5
date	2012.11.17.05.54.51;	author svnexp;	state Exp;
branches;
next	1.4;

1.4
date	2012.10.01.14.45.16;	author tabthorpe;	state Exp;
branches;
next	1.3;

1.3
date	2010.11.08.15.05.11;	author pav;	state Exp;
branches;
next	1.2;

1.2
date	2008.07.25.09.08.40;	author pav;	state Exp;
branches;
next	1.1;

1.1
date	2006.03.16.22.31.26;	author garga;	state Exp;
branches;
next	;


desc
@@


1.6
log
@## SVN ##
## SVN ## Exported commit - http://svnweb.freebsd.org/changeset/base/ 307436
## SVN ## CVS IS DEPRECATED: http://wiki.freebsd.org/CvsIsDeprecated
## SVN ##
## SVN ## ------------------------------------------------------------------------
## SVN ## r307436 | wen | 2012-11-15 07:04:29 +0000 (Thu, 15 Nov 2012) | 8 lines
## SVN ##
## SVN ## - Update to version 2.0
## SVN ## - Update pkg-descr
## SVN ##
## SVN ## PR:		172497
## SVN ## Submitted by:	KATO Tsuguru <tkato432@@yahoo.com>
## SVN ##
## SVN ## Feature safe:	yes
## SVN ##
## SVN ## ------------------------------------------------------------------------
## SVN ##
@
text
@# Created by: Fernan Aguero <fernan@@iib.unsam.edu.ar>
# $FreeBSD: head/biology/lagan/Makefile 307436 2012-11-15 07:04:29Z wen $

PORTNAME=	lagan
PORTVERSION=	2.0
CATEGORIES=	biology
MASTER_SITES=	http://lagan.stanford.edu/lagan_web/
DISTNAME=	${PORTNAME}${PORTVERSION:S/.//}

MAINTAINER=	ports@@FreeBSD.org
COMMENT=	Efficient tools for large-scale multiple alignments of genomic DNA

LICENSE=	GPLv2

USE_PERL5_RUN=	yes
MAKE_JOBS_UNSAFE=yes

SUB_FILES=	pkg-message
SUB_LIST=	LAGAN_DIR="${LAGAN_DIR}"

PLIST_FILES=	${EXECUTABLES:S,^,${PORTNAME}/,} \
		${SCRIPTS:S,^,${PORTNAME}/,} \
		${EXEUTILS:S,^,${PORTNAME}/utils/,} \
		${SCRIPTUTILS:S,^,${PORTNAME}/utils/,} \
		${READMES:S,^,${PORTNAME}/Readmes/,}
PLIST_DIRS=	${PORTNAME}/utils ${PORTNAME}/Readmes
PLIST_DIRSTRY=	${PORTNAME}

LAGAN_DIR=	${PREFIX}/${PORTNAME}

EXECUTABLES=	anchors chaos glocal mlagan order
SCRIPTS=	anal_gloc.pl lagan.pl rechaos.pl slagan.pl
EXEUTILS=	Glue bin2bl bin2mf cextract contigorder cstat dotplot fa2xfa \
		getbounds getcontigpos getlength getoverlap rc scorealign \
		scorecontigs seqmerge
SCRIPTUTILS=	cmerge2.pl draft.pl mextract.pl mf2bin.pl mpretty.pl \
		mproject.pl mrun.pl mrunfile.pl mrunpairs.pl mviz.pl
READMES=	README.FIRST README.chaos README.lagan README.mlagan \
		README.tools README.shuffle

post-patch:
	@@${FIND} ${WRKSRC} -name "Makefile" | ${XARGS} ${REINPLACE_CMD} -e \
		'/^CC/s|^|#| ; \
		 /^CFLAGS/s|^|#| ; \
		 s|$$(CC) -o|$$(CC) $$(CFLAGS) -o| ; \
		 s|$$(CPP) -o|$$(CXX) $$(CXXFLAGS) -o| ; \
		 s|$$(CLINKER) $$(OPTFLAGS)|$$(CXX) $$(LDFLAGS)|'

do-install:
	@@${MKDIR} ${LAGAN_DIR}
.for exe in ${EXECUTABLES}
	${INSTALL_PROGRAM} ${WRKSRC}/${exe} ${LAGAN_DIR}
.endfor
.for script in ${SCRIPTS}
	${INSTALL_SCRIPT} ${WRKSRC}/${script} ${LAGAN_DIR}
.endfor
	@@${MKDIR} ${LAGAN_DIR}/utils
.for exeutil in ${EXEUTILS}
	${INSTALL_PROGRAM} ${WRKSRC}/utils/${exeutil} ${LAGAN_DIR}/utils
.endfor
.for scriptutil in ${SCRIPTUTILS}
	${INSTALL_SCRIPT} ${WRKSRC}/utils/${scriptutil} ${LAGAN_DIR}/utils
.endfor
	@@${MKDIR} ${LAGAN_DIR}/Readmes
.for readme in ${READMES}
	${INSTALL_DATA} ${WRKSRC}/Readmes/${readme} ${LAGAN_DIR}/Readmes
.endfor
	@@${CAT} ${PKGMESSAGE}

.include <bsd.port.mk>
@


1.5
log
@Switch exporter over
@
text
@d2 1
a2 1
# $FreeBSD: head/biology/lagan/Makefile 305130 2012-10-01 14:45:16Z tabthorpe $
d5 1
a5 1
PORTVERSION=	1.2
d13 2
a14 1
LAGAN_DIR=	${PREFIX}/${PORTNAME}
d16 2
d19 11
a29 1
SUB_LIST=	LAGAN_DIR=${LAGAN_DIR}
d38 2
a39 3

CC:=		${CC} ${CFLAGS}
CPP=		${CXX} ${CXXFLAGS}
d42 6
a47 2
	@@${REINPLACE_CMD} -E 's,^(CC|CPP) =,\1 ?=,g' \
		${WRKSRC}/Makefile
a50 1
	${CP} -R ${WRKSRC}/Readmes ${LAGAN_DIR}
d64 4
@


1.4
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
# $FreeBSD$
@


1.3
log
@- Unbreak build: CPP is now part of MAKE_ENV

Reported by:	pointyhat
@
text
@d1 1
a1 4
# New ports collection makefile for:	lagan
# Date created:		07 Dec 2005
# Whom:	      		Fernan Aguero <fernan@@iib.unsam.edu.ar>
#
a2 1
#
d10 1
a10 1
MAINTAINER=	fernan@@iib.unsam.edu.ar
@


1.2
log
@- Remove duplicates from MAKE_ENV after inclusion of CC and CXX in default MAKE_ENV
@
text
@d31 1
a31 1
MAKE_ENV+=	CPP="${CXX} ${CXXFLAGS}"
@


1.1
log
@Add lagan 1.2, efficient tools for large-scale multiple alignments of
genomic DNA.

PR:		ports/93058
Submitted by:	Fernan Aguero <fernan@@iib.unsam.edu.ar>
@
text
@d30 2
a31 1
MAKE_ENV+=	CC="${CC} ${CFLAGS}" CPP="${CXX} ${CXXFLAGS}"
@

