Date: Tue, 20 Nov 2007 12:24:06 +1100 (EST) From: Tony Maher <anthony.maher@uts.edu.au> To: FreeBSD-gnats-submit@FreeBSD.org Subject: ports/118142: New port: biology/mummer Message-ID: <200711200124.lAK1O63B027952@karma.internal> Resent-Message-ID: <200711200200.lAK206XJ088869@freefall.freebsd.org>
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>Number: 118142 >Category: ports >Synopsis: New port: biology/mummer >Confidential: no >Severity: non-critical >Priority: low >Responsible: freebsd-ports-bugs >State: open >Quarter: >Keywords: >Date-Required: >Class: change-request >Submitter-Id: current-users >Arrival-Date: Tue Nov 20 02:00:05 UTC 2007 >Closed-Date: >Last-Modified: >Originator: Tony Maher >Release: FreeBSD 6.2-RELEASE-p7 i386 >Organization: >Environment: System: FreeBSD karma.internal 6.2-RELEASE-p7 FreeBSD 6.2-RELEASE-p7 #6: Fri Aug 24 21:40:36 EST 2007 root@karma.internal:/var/obj/usr/src/sys/KARMA i386 >Description: New port MUMmer (http://mummer.sourceforge.net/) "MUMmer is a system for rapidly aligning entire genomes, whether in complete or draft form." I want it as a prerequisite for: AMOS Assembler. A Modular Open Source Assembler. (http://amos.sourceforge.net) Will send a port for this soon. >How-To-Repeat: >Fix: # 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@uts.edu.au XCOMMENT= A modular system for rapid whole genome alignment X XUSE_GMAKE= 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 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 >Release-Note: >Audit-Trail: >Unformatted:
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