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.

6 files changed, 96 insertions, 1 deletions

diff --git a/biology/Makefile b/biology/Makefile
index edf2729c2eb..e6179d39743 100644
--- a/biology/Makefile
+++ b/biology/Makefile
@@ -1,4 +1,4 @@
-# $NetBSD: Makefile,v 1.32 2011/10/05 22:29:44 ryoon Exp $
+# $NetBSD: Makefile,v 1.33 2011/10/31 21:28:03 brook Exp $
 #
 
 COMMENT=	Software for the biological sciences
@@ -26,6 +26,7 @@ SUBDIR+=	nut
 SUBDIR+=	openbabel
 SUBDIR+=	pdbalign
 SUBDIR+=	phylip
+SUBDIR+=	primer3
 SUBDIR+=	profit
 SUBDIR+=	puzzle
 SUBDIR+=	py-mol
diff --git a/biology/primer3/DESCR b/biology/primer3/DESCR
new file mode 100644
index 00000000000..d4913dbf79f
--- /dev/null
+++ b/biology/primer3/DESCR
@@ -0,0 +1,24 @@
+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
diff --git a/biology/primer3/Makefile b/biology/primer3/Makefile
new file mode 100644
index 00000000000..f2a323dc54d
--- /dev/null
+++ b/biology/primer3/Makefile
@@ -0,0 +1,39 @@
+# $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"
diff --git a/biology/primer3/PLIST b/biology/primer3/PLIST
new file mode 100644
index 00000000000..0d0c0cfd68a
--- /dev/null
+++ b/biology/primer3/PLIST
@@ -0,0 +1,10 @@
+@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
diff --git a/biology/primer3/distinfo b/biology/primer3/distinfo
new file mode 100644
index 00000000000..b19efd7245f
--- /dev/null
+++ b/biology/primer3/distinfo
@@ -0,0 +1,6 @@
+$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
diff --git a/biology/primer3/patches/patch-src_primer3__boulder__main.c b/biology/primer3/patches/patch-src_primer3__boulder__main.c
new file mode 100644
index 00000000000..61d0bacbbd4
--- /dev/null
+++ b/biology/primer3/patches/patch-src_primer3__boulder__main.c
@@ -0,0 +1,15 @@
+$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;