Initial import of primer3.

Primer3 is a widely used program for designing PCR primers (PCR =
"Polymerase Chain Reaction").  PCR is an essential and ubiquitous tool
in genetics and molecular biology.  Primer3 can also design
hybridization probes and sequencing primers.

Status:

Vendor Tag:	TNF
Release Tags:	pkgsrc-base


(brook)

Primer3 is a widely used program for designing PCR primers (PCR =
"Polymerase Chain Reaction").  PCR is an essential and ubiquitous tool
in genetics and molecular biology.  Primer3 can also design
hybridization probes and sequencing primers.

Primer3 picks primers for PCR reactions, considering as criteria: o

- oligonucleotide melting temperature, size, GC content, and
  primer-dimer possibilities,
- PCR product size,
- positional constraints within the source (template) sequence,
- possibilities for ectopic priming (amplifying the wrong sequence), and
- many 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.

Whitehead Institute for Biomedical Research provides a basic web-based
front end to primer3 named primer3web at http://fokker.wi.mit.edu/

Wageningen University Laboratory of Bioinformatics provides a enhanced
web-based front end to primer3 named primer3plus at
http://www.bioinformatics.nl/cgi-bin/primer3plus/primer3plus.cgi

# $NetBSD: Makefile,v 1.1.1.1 2011/10/31 21:25:57 brook Exp $
#

VERS=		2.2.3

DISTNAME=	primer3-${VERS}
CATEGORIES=	biology
MASTER_SITES=	${MASTER_SITE_SOURCEFORGE:=primer3/}

MAINTAINER=	pkgsrc-users@NetBSD.org
HOMEPAGE=	http://primer3.sourceforge.net/
COMMENT=	Design PCR primers
LICENSE=	gnu-gpl-v2

PKG_DESTDIR_SUPPORT=	user-destdir

USE_LANGUAGES=	c c++
USE_TOOLS+=	gmake
BUILD_DIRS=	src
NO_CONFIGURE=	yes

BINFILES+=	long_seq_tm_test ntdpal ntthal oligotm primer3_core
DOCFILES+=	primer3_manual.htm primer3_v1_1_4_default_settings.txt
DOCFILES+=	primer3web_v0_4_0_default_settings.txt example

BINDIR=		${PREFIX}/bin
DOCDIR=		${PREFIX}/share/doc/primer3

INSTALLATION_DIRS+=	${BINDIR} ${DOCDIR}

do-install:
.for f in ${BINFILES}
	${INSTALL_DATA} ${WRKSRC}/src/${f} ${DESTDIR}${BINDIR}
.endfor
.for f in ${DOCFILES}
	${INSTALL_DATA} ${WRKSRC}/${f} ${DESTDIR}${DOCDIR}
.endfor

.include "../../mk/bsd.pkg.mk"

@comment $NetBSD: PLIST,v 1.1.1.1 2011/10/31 21:25:57 brook Exp $
bin/long_seq_tm_test
bin/ntdpal
bin/ntthal
bin/oligotm
bin/primer3_core
share/doc/primer3/primer3_manual.htm
share/doc/primer3/primer3_v1_1_4_default_settings.txt
share/doc/primer3/primer3web_v0_4_0_default_settings.txt
share/doc/primer3/example

$NetBSD: distinfo,v 1.1.1.1 2011/10/31 21:25:57 brook Exp $

SHA1 (primer3-2.2.3.tar.gz) = 20c6a00455b86a5712c1e297930f2624fca45881
RMD160 (primer3-2.2.3.tar.gz) = 040b41649f5bfc17214502b2ba5e98d1a5afd73f
Size (primer3-2.2.3.tar.gz) = 2284282 bytes
SHA1 (patch-src_primer3__boulder__main.c) = a9228eb3f8f1969a6bc332f828db2def7cf00005

$NetBSD: patch-src_primer3__boulder__main.c,v 1.1.1.1 2011/10/31 21:25:57 brook Exp $

getopt_long_only is not very portable; use getopt_long instead.

--- src/primer3_boulder_main.c.orig	2010-07-08 17:58:25.000000000 +0000
+++ src/primer3_boulder_main.c
@@ -133,7 +133,7 @@ main(int argc, char *argv[]) 
   
   /* Read in the flags provided with the program call */
   opterr = 0;
-  while ((opt = getopt_long_only(argc, argv, "", long_options, &option_index)) != -1) {
+  while ((opt = getopt_long(argc, argv, "", long_options, &option_index)) != -1) {
     switch (opt) {
     case 'a':
       about = 1;