freebsd-ports/biology/mummer/Makefile

# Created by: Tony Maher
# $FreeBSD$

PORTNAME=	mummer
PORTVERSION=	3.23
CATEGORIES=	biology
MASTER_SITES=	SF
DISTNAME=	MUMmer${PORTVERSION}

MAINTAINER=	sylvio@FreeBSD.org
COMMENT=	A modular system for rapid whole genome alignment

USES=		gmake

PROGRAMS=	annotate combineMUMs delta-filter gaps \
		mgaps mummer repeat-match show-aligns \
		show-coords show-diff show-snps show-tiling
SCRIPTS=	dnadiff exact-tandems mapview mummerplot nucmer \
		nucmer2xfig promer run-mummer1 run-mummer3
DOCUMENTS=	COPYRIGHT INSTALL LICENSE README

OPTIONS_DEFINE=	DOCS

.include <bsd.port.options.mk>

do-install:
	${INSTALL_PROGRAM} ${PROGRAMS:S|^|${WRKSRC}/|} ${STAGEDIR}${PREFIX}/bin
	${INSTALL_SCRIPT} ${SCRIPTS:S|^|${WRKSRC}/|} ${STAGEDIR}${PREFIX}/bin
	@${MKDIR} ${STAGEDIR}${DOCSDIR}
	${INSTALL_DATA} ${DOCUMENTS:S|^|${WRKSRC}/|} ${STAGEDIR}${DOCSDIR}

.include <bsd.port.mk>
Add NO_STAGE all over the place in preparation for the staging support (cat: biology) 2013-09-20 17:55:44 +02:00			`# Created by: Tony Maher`
MUMmer is a modular system for the rapid whole genome alignment of finished or draft sequence. This package provides an efficient suffix tree library, seed-and-extend alignment, SNP detection, repeat detection, and visualization tools. WWW: http://mummer.sourceforge.net/ PR: ports/118142 Submitted by: Tony Maher 2007-12-14 21:54:47 +01:00			`# $FreeBSD$`

			`PORTNAME= mummer`
- Update to 3.23 2012-01-17 01:51:39 +01:00			`PORTVERSION= 3.23`
MUMmer is a modular system for the rapid whole genome alignment of finished or draft sequence. This package provides an efficient suffix tree library, seed-and-extend alignment, SNP detection, repeat detection, and visualization tools. WWW: http://mummer.sourceforge.net/ PR: ports/118142 Submitted by: Tony Maher 2007-12-14 21:54:47 +01:00			`CATEGORIES= biology`
			`MASTER_SITES= SF`
			`DISTNAME= MUMmer${PORTVERSION}`

- Update my mail address to FreeBSD Approved by: miwi (mentor) 2009-11-27 23:52:30 +01:00			`MAINTAINER= sylvio@FreeBSD.org`
MUMmer is a modular system for the rapid whole genome alignment of finished or draft sequence. This package provides an efficient suffix tree library, seed-and-extend alignment, SNP detection, repeat detection, and visualization tools. WWW: http://mummer.sourceforge.net/ PR: ports/118142 Submitted by: Tony Maher 2007-12-14 21:54:47 +01:00			`COMMENT= A modular system for rapid whole genome alignment`

- Convert USE_GMAKE to USES 2014-03-13 08:41:34 +01:00			`USES= gmake`
MUMmer is a modular system for the rapid whole genome alignment of finished or draft sequence. This package provides an efficient suffix tree library, seed-and-extend alignment, SNP detection, repeat detection, and visualization tools. WWW: http://mummer.sourceforge.net/ PR: ports/118142 Submitted by: Tony Maher 2007-12-14 21:54:47 +01:00
			`PROGRAMS= annotate combineMUMs delta-filter gaps \`
			`mgaps mummer repeat-match show-aligns \`
			`show-coords show-diff show-snps show-tiling`
			`SCRIPTS= dnadiff exact-tandems mapview mummerplot nucmer \`
			`nucmer2xfig promer run-mummer1 run-mummer3`
			`DOCUMENTS= COPYRIGHT INSTALL LICENSE README`

Remove trailing whitespaces from category biology 2014-02-21 14:35:26 +01:00			`OPTIONS_DEFINE= DOCS`
According to the Porter's Handbook (5.12.2.3.) default options must be added to OPTIONS_DEFINE. This policy has been implemented only recently that's why we have many ports violating this policy. This patch adds the default options specified in the Porter's Handbook to OPTIONS_DEFINE where they are being used. Ports maintained by gnome@FreeBSD.org, kde@FreeBSD.org and x11@FreeBSD.org have been excluded. Approved by: portmgr (bapt) 2014-02-10 14:54:26 +01:00
Convert biology to MDOCS and MEXAMPLES 2014-01-03 16:46:52 +01:00			`.include <bsd.port.options.mk>`

MUMmer is a modular system for the rapid whole genome alignment of finished or draft sequence. This package provides an efficient suffix tree library, seed-and-extend alignment, SNP detection, repeat detection, and visualization tools. WWW: http://mummer.sourceforge.net/ PR: ports/118142 Submitted by: Tony Maher 2007-12-14 21:54:47 +01:00			`do-install:`
- add stage support 2014-06-01 12:54:33 +02:00			`${INSTALL_PROGRAM} ${PROGRAMS:S\|^\|${WRKSRC}/\|} ${STAGEDIR}${PREFIX}/bin`
			`${INSTALL_SCRIPT} ${SCRIPTS:S\|^\|${WRKSRC}/\|} ${STAGEDIR}${PREFIX}/bin`
			`@${MKDIR} ${STAGEDIR}${DOCSDIR}`
			`${INSTALL_DATA} ${DOCUMENTS:S\|^\|${WRKSRC}/\|} ${STAGEDIR}${DOCSDIR}`
MUMmer is a modular system for the rapid whole genome alignment of finished or draft sequence. This package provides an efficient suffix tree library, seed-and-extend alignment, SNP detection, repeat detection, and visualization tools. WWW: http://mummer.sourceforge.net/ PR: ports/118142 Submitted by: Tony Maher 2007-12-14 21:54:47 +01:00
			`.include <bsd.port.mk>`