From owner-freebsd-ports Sun Feb 24 19: 0:24 2002 Delivered-To: freebsd-ports@hub.freebsd.org Received: from freefall.freebsd.org (freefall.FreeBSD.org [216.136.204.21]) by hub.freebsd.org (Postfix) with ESMTP id 60DDE37B417 for ; Sun, 24 Feb 2002 19:00:02 -0800 (PST) Received: (from gnats@localhost) by freefall.freebsd.org (8.11.6/8.11.6) id g1P302E78055; Sun, 24 Feb 2002 19:00:02 -0800 (PST) (envelope-from gnats) Received: from yellow.biolateral.com.au (yellow.biolateral.com.au [129.78.217.60]) by hub.freebsd.org (Postfix) with ESMTP id DCDCE37B417 for ; Sun, 24 Feb 2002 18:55:58 -0800 (PST) Received: (from tonym@localhost) by yellow.biolateral.com.au (8.11.6/8.11.6) id g1P2tvB17817; Mon, 25 Feb 2002 13:55:57 +1100 (EST) (envelope-from tonym) Message-Id: <200202250255.g1P2tvB17817@yellow.biolateral.com.au> Date: Mon, 25 Feb 2002 13:55:57 +1100 (EST) From: Tony Maher Reply-To: Tony Maher To: FreeBSD-gnats-submit@freebsd.org X-Send-Pr-Version: 3.113 Subject: ports/35298: New port: biology/primer3 Sender: owner-freebsd-ports@FreeBSD.ORG Precedence: bulk List-ID: List-Archive: (Web Archive) List-Help: (List Instructions) List-Subscribe: List-Unsubscribe: X-Loop: FreeBSD.org >Number: 35298 >Category: ports >Synopsis: New port: biology/primer3 >Confidential: no >Severity: non-critical >Priority: low >Responsible: freebsd-ports >State: open >Quarter: >Keywords: >Date-Required: >Class: change-request >Submitter-Id: current-users >Arrival-Date: Sun Feb 24 19:00:02 PST 2002 >Closed-Date: >Last-Modified: >Originator: Tony Maher >Release: FreeBSD 4.5-STABLE i386 >Organization: BioLateral >Environment: System: FreeBSD dt.home 4.5-STABLE FreeBSD 4.5-STABLE #0: Fri Feb 22 12:29:39 EST 2002 root@dt.home:/usr/obj/usr/src/sys/DT i386 >Description: New port: biology/primer3 ---------------------------------------------------------------------- Primer3 picks primers for PCR reactions, considering as criteria: o oligonucleotide melting temperature, size, GC content, and primer-dimer possibilities, o PCR product size, o positional constraints within the source sequence, and o miscellaneous other constraints. All of these criteria are user-specifiable as constraints, and some are specifiable as terms in an objective function that characterizes an optimal primer pair." - from the README file WWW: http://www-genome.wi.mit.edu/genome_software/other/primer3.html ---------------------------------------------------------------------- NOTES: The licence is similar to old BSD with advertising clause: 3. All advertising materials mentioning features or use of this software must display the following acknowledgment: This product includes software developed by the Whitehead Institute for Biomedical Research. Does this affect packaging or putting on CDROM? >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: # # primer3 # primer3/pkg-descr # primer3/distinfo # primer3/Makefile # primer3/pkg-comment # primer3/pkg-plist # echo c - primer3 mkdir -p primer3 > /dev/null 2>&1 echo x - primer3/pkg-descr sed 's/^X//' >primer3/pkg-descr << 'END-of-primer3/pkg-descr' X"Primer3 is a complete rewrite of the original PRIMER program X(Primer 0.5), written by Steve Lincoln, Mark Daly, and Eric XLander. See DIFFERENCES FROM EARLIER VERSIONS for a discussion Xof how Primer3 differs from its predecessors, Primer 0.5 and XPrimer v2. X XPrimer3 picks primers for PCR reactions, considering as criteria: X Xo oligonucleotide melting temperature, size, GC content, X and primer-dimer possibilities, Xo PCR product size, Xo positional constraints within the source sequence, and Xo miscellaneous other constraints. X XAll of these criteria are user-specifiable as constraints, and Xsome are specifiable as terms in an objective function that Xcharacterizes an optimal primer pair." X- from the README file X XWWW: http://www-genome.wi.mit.edu/genome_software/other/primer3.html X X-- XTony Maher END-of-primer3/pkg-descr Echo x - primer3/distinfo sed 's/^X//' >primer3/distinfo << 'END-of-primer3/distinfo' XMD5 (primer3_0_9_test.tar.gz) = 1ae09013c982eb67953cc4dd5b837088 END-of-primer3/distinfo echo x - primer3/Makefile sed 's/^X//' >primer3/Makefile << 'END-of-primer3/Makefile' X# New ports collection makefile for: primer3 X# Date created: 25 February 2002 X# Whom: Tony Maher X# X# $FreeBSD$ X# X XPORTNAME= primer3 XPORTVERSION= 0.9 XCATEGORIES= biology XMASTER_SITES= http://www-genome.wi.mit.edu/ftp/distribution/software/ XDISTNAME= ${PORTNAME}_0_9_test X XMAINTAINER= tonym@biolateral.com.au X XWRKSRC= ${WRKDIR}/${DISTNAME}/src X XCPIO= cpio --quiet -pdum -R XDOCUMENTS= README example XCGI-EXAMPLES= primer3_www.cgi primer3_www_help.html \ X primer3_www_results.cgi primer3_www_results_help.html X Xpre-configure: X @${PERL} -pi.orig \ X -e 's#^CFLAGS.*#CFLAGS += \$$\(CC_OPTS\)#;' \ X -e 's#CC_OPTS = -g#CC_OPTS =#;' \ X -e 's#LDFLAGS = -g#LDFLAGS ?=#;' \ X -e 's#^WHITEHEAD_SPECIFIC_HACK.*##;' \ X ${WRKDIR}/${DISTNAME}/src/Makefile X Xdo-install: X @${INSTALL_PROGRAM} ${WRKSRC}/primer3_core ${PREFIX}/bin/primer3 X @${MKDIR} ${DATADIR} X @${INSTALL_DATA} ${WRKDIR}/${DISTNAME}/Copyright ${DATADIR} X.for file in ${CGI-EXAMPLES} X @${INSTALL_DATA} ${WRKSRC}/${file} ${DATADIR} X.endfor X.if !defined(NOPORTDOCS) X @${MKDIR} ${DOCSDIR} X.for file in ${DOCUMENTS} X @${INSTALL_DATA} ${WRKDIR}/${DISTNAME}/${file} ${DOCSDIR} X.endfor X @${MKDIR} ${EXAMPLESDIR} X @cd ${WRKDIR}/${DISTNAME}/test && find * | \ X ${CPIO} ${SHAREOWN}:${SHAREGRP} ${EXAMPLESDIR} X.endif X Xpost-install: X @${CAT} ${DATADIR}/Copyright X X.include END-of-primer3/Makefile echo x - primer3/pkg-comment sed 's/^X//' >primer3/pkg-comment << 'END-of-primer3/pkg-comment' XPrimer3 helps to choose primers for PCR reactions END-of-primer3/pkg-comment echo x - primer3/pkg-plist sed 's/^X//' >primer3/pkg-plist << 'END-of-primer3/pkg-plist' X%%PORTDOCS%%share/doc/primer3/README X%%PORTDOCS%%share/doc/primer3/example X%%PORTDOCS%%share/examples/primer3/dpal_gen.pl X%%PORTDOCS%%share/examples/primer3/dpal_input X%%PORTDOCS%%share/examples/primer3/dpal_long_input X%%PORTDOCS%%share/examples/primer3/dpal_long_score_output X%%PORTDOCS%%share/examples/primer3/dpal_output X%%PORTDOCS%%share/examples/primer3/dpal_score_output X%%PORTDOCS%%share/examples/primer3/dpal_test.pl X%%PORTDOCS%%share/examples/primer3/long_seq_input X%%PORTDOCS%%share/examples/primer3/long_seq_output X%%PORTDOCS%%share/examples/primer3/not_for_production.lib X%%PORTDOCS%%share/examples/primer3/primer1_input X%%PORTDOCS%%share/examples/primer3/primer1_list_last/AGAG.for X%%PORTDOCS%%share/examples/primer3/primer1_list_last/AGAG.rev X%%PORTDOCS%%share/examples/primer3/primer1_list_last/SP01-02.txt.for X%%PORTDOCS%%share/examples/primer3/primer1_list_last/SP01-02.txt.rev X%%PORTDOCS%%share/examples/primer3/primer1_list_last/SP01-03.txt.for X%%PORTDOCS%%share/examples/primer3/primer1_list_last/SP01-03.txt.rev X%%PORTDOCS%%share/examples/primer3/primer1_list_last/SP01-06.txt.for X%%PORTDOCS%%share/examples/primer3/primer1_list_last/SP01-06.txt.rev X%%PORTDOCS%%share/examples/primer3/primer1_list_last/SP01-19.txt.for X%%PORTDOCS%%share/examples/primer3/primer1_list_last/SP01-19.txt.rev X%%PORTDOCS%%share/examples/primer3/primer1_list_last/SP01-21.txt.for X%%PORTDOCS%%share/examples/primer3/primer1_list_last/SP01-21.txt.rev X%%PORTDOCS%%share/examples/primer3/primer1_list_last/SP04-07.txt.for X%%PORTDOCS%%share/examples/primer3/primer1_list_last/SP04-07.txt.rev X%%PORTDOCS%%share/examples/primer3/primer1_list_last/included_test.for X%%PORTDOCS%%share/examples/primer3/primer1_list_last/included_test.rev X%%PORTDOCS%%share/examples/primer3/primer1_list_last/included_test_w_middle.for X%%PORTDOCS%%share/examples/primer3/primer1_list_last/included_test_w_middle.int X%%PORTDOCS%%share/examples/primer3/primer1_list_last/long_seq.for X%%PORTDOCS%%share/examples/primer3/primer1_list_last/included_test_w_middle.rev X%%PORTDOCS%%share/examples/primer3/primer1_list_last/long_seq.rev X%%PORTDOCS%%share/examples/primer3/primer1_list_last/targets_test.for X%%PORTDOCS%%share/examples/primer3/primer1_list_last/targets_test.rev X%%PORTDOCS%%share/examples/primer3/primer1_output X%%PORTDOCS%%share/examples/primer3/primer_boundary1_formated_output X%%PORTDOCS%%share/examples/primer3/primer_boundary1_input X%%PORTDOCS%%share/examples/primer3/primer_boundary1_output X%%PORTDOCS%%share/examples/primer3/primer_boundary_formated_output X%%PORTDOCS%%share/examples/primer3/primer_boundary_input X%%PORTDOCS%%share/examples/primer3/primer_boundary_output X%%PORTDOCS%%share/examples/primer3/primer_check_input X%%PORTDOCS%%share/examples/primer3/primer_check_output 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