ports/118142: New port: biology/mummer

[Tony Maher]

The following reply was made to PR ports/118142; it has been noted by GNATS.

From: Tony Maher <anthony.maher at uts.edu.au>
To: bug-followup at FreeBSD.org
Cc: Anthony.Maher at uts.edu.au
Subject: Re: ports/118142: New port: biology/mummer
Date: Tue, 20 Nov 2007 14:58:45 +1100 (EST)

 Make port respect CFLAGS
 Note dependency on Perl.
 The following is new shar file - pls ignore the first one.
 
 # This is a shell archive.  Save it in a file, remove anything before
 # this line, and then unpack it by entering "sh file".  Note, it may
 # create directories; files and directories will be owned by you and
 # have default permissions.
 #
 # This archive contains:
 #
 #	mummer
 #	mummer/Makefile
 #	mummer/pkg-plist
 #	mummer/pkg-descr
 #	mummer/distinfo
 #
 echo c - mummer
 mkdir -p mummer > /dev/null 2>&1
 echo x - mummer/Makefile
 sed 's/^X//' >mummer/Makefile << 'END-of-mummer/Makefile'
 X# ex:ts=8
 X# New ports collection makefile for:	MUMmer
 X# Date created:				20 November 2007
 X# Whom:					Tony Maher
 X#
 X# $FreeBSD$
 X#
 X
 XPORTNAME=	mummer
 XPORTVERSION=	3.20
 XCATEGORIES=	biology
 XMASTER_SITES=	${MASTER_SITE_SOURCEFORGE}
 XMASTER_SITE_SUBDIR=${PORTNAME}
 XDISTNAME=	MUMmer${PORTVERSION}
 X
 XMAINTAINER=	Anthony.Maher at uts.edu.au
 XCOMMENT=	A modular system for rapid whole genome alignment
 X
 XUSE_GMAKE=	yes
 XUSE_PERL5=	yes
 X
 XPROGRAMS=	annotate combineMUMs delta-filter gaps \
 X		mgaps mummer repeat-match show-aligns \
 X		show-coords show-diff show-snps show-tiling
 XSCRIPTS=	dnadiff exact-tandems mapview mummerplot nucmer \
 X		nucmer2xfig promer run-mummer1 run-mummer3
 XDOCUMENTS=	COPYRIGHT INSTALL LICENSE README
 X
 Xpost-configure:
 X	@${REINPLACE_CMD} -e \
 X		s'#^CPPFLAGS = -Wall -O3#CPPFLAGS = $${CFLAGS}#;' \
 X		${WRKSRC}/${MAKEFILE}
 X
 Xdo-install:
 X.for program in ${PROGRAMS}
 X	(cd ${WRKSRC} && ${INSTALL_PROGRAM} ${program} ${PREFIX}/bin)
 X.endfor
 X
 X.for script in ${SCRIPTS}
 X	(cd ${WRKSRC} && ${INSTALL_SCRIPT} ${script} ${PREFIX}/bin)
 X.endfor
 X
 X.if !defined(NOPORTDOCS)
 X	@${MKDIR} ${DOCSDIR}
 X.for doc in ${DOCUMENTS}
 X	(cd ${WRKSRC} && ${INSTALL_DATA} ${doc} ${DOCSDIR})
 X.endfor
 X.endif
 X
 X.include <bsd.port.mk>
 END-of-mummer/Makefile
 echo x - mummer/pkg-plist
 sed 's/^X//' >mummer/pkg-plist << 'END-of-mummer/pkg-plist'
 Xbin/annotate
 Xbin/combineMUMs
 Xbin/delta-filter
 Xbin/dnadiff
 Xbin/exact-tandems
 Xbin/gaps
 Xbin/mapview
 Xbin/mgaps
 Xbin/mummer
 Xbin/mummerplot
 Xbin/nucmer
 Xbin/nucmer2xfig
 Xbin/promer
 Xbin/repeat-match
 Xbin/run-mummer1
 Xbin/run-mummer3
 Xbin/show-aligns
 Xbin/show-coords
 Xbin/show-diff
 Xbin/show-snps
 Xbin/show-tiling
 X%%PORTDOCS%%%%DOCSDIR%%/COPYRIGHT
 X%%PORTDOCS%%%%DOCSDIR%%/INSTALL
 X%%PORTDOCS%%%%DOCSDIR%%/LICENSE
 X%%PORTDOCS%%%%DOCSDIR%%/README
 X%%PORTDOCS%%@dirrm %%DOCSDIR%%
 END-of-mummer/pkg-plist
 echo x - mummer/pkg-descr
 sed 's/^X//' >mummer/pkg-descr << 'END-of-mummer/pkg-descr'
 X"MUMmer is a modular system for the rapid whole genome alignment of finished
 X or draft sequence. This package provides an efficient suffix tree library,
 X seed-and-extend alignment, SNP detection, repeat detection, and
 X visualization tools".
 X
 XWWW:	http://mummer.sourceforge.net/
 END-of-mummer/pkg-descr
 echo x - mummer/distinfo
 sed 's/^X//' >mummer/distinfo << 'END-of-mummer/distinfo'
 XMD5 (MUMmer3.20.tar.gz) = 4c3f6e528df50f8dfd3a7cd0ea224306
 XSHA256 (MUMmer3.20.tar.gz) = 9c7880b4ce25ef3c6bed9ccdc26f1c4d7e74eb0ef1ce403907790c0f96c0f260
 XSIZE (MUMmer3.20.tar.gz) = 3155446
 END-of-mummer/distinfo
 exit