From c293387ca844e756d0a924d4fa3e35c3f99290d7 Mon Sep 17 00:00:00 2001 From: brook Date: Mon, 31 Oct 2011 21:25:57 +0000 Subject: 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. --- biology/Makefile | 3 +- biology/primer3/DESCR | 24 +++++++++++++ biology/primer3/Makefile | 39 ++++++++++++++++++++++ biology/primer3/PLIST | 10 ++++++ biology/primer3/distinfo | 6 ++++ .../patches/patch-src_primer3__boulder__main.c | 15 +++++++++ 6 files changed, 96 insertions(+), 1 deletion(-) create mode 100644 biology/primer3/DESCR create mode 100644 biology/primer3/Makefile create mode 100644 biology/primer3/PLIST create mode 100644 biology/primer3/distinfo create mode 100644 biology/primer3/patches/patch-src_primer3__boulder__main.c (limited to 'biology') 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; -- cgit v1.2.3