Add dna-qc 1993.07.26, a quality control algorithm for DNA

sequencing projects.

PR:		32998
Submitted by:	Tony Maher <tonym@biolateral.com.au>

6 files changed, 93 insertions, 0 deletions

diff --git a/biology/dna-qc/Makefile b/biology/dna-qc/Makefile
new file mode 100644
index 000000000000..700cc1ca2122
--- /dev/null
+++ b/biology/dna-qc/Makefile
@@ -0,0 +1,45 @@
+# New ports collection makefile for:	dna-qc
+# Date created:				25 Novemeber 2001
+# Whom:					Tony Maher <tonym@biolateral.com.au>
+#
+# $FreeBSD$
+#
+
+PORTNAME=	dna-qc
+PORTVERSION=	1993.07.26
+CATEGORIES=	biology
+MASTER_SITES=	ftp://ftp.tigr.org/pub/software/qc/
+DISTNAME=	qc
+EXTRACT_SUFX=	.tar.Z
+
+MAINTAINER=	tonym@biolateral.com.au
+
+NO_WRKSUBDIR=	true
+
+EXAMPLES=	README script.compare script.limits \
+		bact.all chromosomeIII.all human.all worm.all
+PROGRAMS=	counter hybridize normalize random_clip random_line
+
+post-patch:
+	@${PERL} -pi -e 's,^CFLAGS,#CFLAGS,' ${WRKSRC}/Makefile
+	@${PERL} -pi -e 's,malloc.h,stdlib.h,' ${WRKSRC}/normalize.c
+	@${PERL} -pi -e 's,fname\*,fname,' ${WRKSRC}/random_line.c
+	@${PERL} -pi -e 's,static void allocate_pool,void allocate_pool,' \
+		${WRKSRC}/stringpool.c
+
+do-install:
+.for file in ${PROGRAMS}
+	${INSTALL_PROGRAM} ${WRKSRC}/${file} ${PREFIX}/bin
+	strip ${PREFIX}/bin/${file}
+.endfor
+.if !defined(NOPORTDOCS)
+	@${MKDIR} ${DOCSDIR}
+	${INSTALL_DATA} ${WRKSRC}/qc_doc/* ${DOCSDIR}
+	${INSTALL_DATA} ${WRKSRC}/surprize_doc/* ${DOCSDIR}
+	@${MKDIR} ${EXAMPLESDIR}
+.for file in ${EXAMPLES}
+	${INSTALL_DATA} ${WRKSRC}/${file} ${EXAMPLESDIR}
+.endfor
+.endif
+
+.include <bsd.port.mk>
diff --git a/biology/dna-qc/distinfo b/biology/dna-qc/distinfo
new file mode 100644
index 000000000000..7da08044c989
--- /dev/null
+++ b/biology/dna-qc/distinfo
@@ -0,0 +1,2 @@
+MD5 (qc.tar.Z) = 30dc287fa9c7c8e818d4ce0a34b86422
+MD5 (hyb2dis.txt) = e5b8260c84a822cb0deff264f01331b8
diff --git a/biology/dna-qc/files/patch-hybridize.c b/biology/dna-qc/files/patch-hybridize.c
new file mode 100644
index 000000000000..45dae76fc31e
--- /dev/null
+++ b/biology/dna-qc/files/patch-hybridize.c
@@ -0,0 +1,12 @@
+$FreeBSD$
+
+--- hybridize.c.orig	Sat Nov 24 21:25:04 2001
++++ hybridize.c	Sat Nov 24 21:25:35 2001
+@@ -54,6 +54,7 @@
+ extern unsigned array_to_base_4();
+ extern unsigned string_to_base_4();
+ extern int dna2i();
++double logl();
+ int *read_file();
+ 
+ main(argc, argv)
diff --git a/biology/dna-qc/pkg-comment b/biology/dna-qc/pkg-comment
new file mode 100644
index 000000000000..38f03537d32c
--- /dev/null
+++ b/biology/dna-qc/pkg-comment
@@ -0,0 +1 @@
+A quality control algorithm for DNA sequencing projects
diff --git a/biology/dna-qc/pkg-descr b/biology/dna-qc/pkg-descr
new file mode 100644
index 000000000000..7018f40d8854
--- /dev/null
+++ b/biology/dna-qc/pkg-descr
@@ -0,0 +1,8 @@
+"relevant reference:
+White, O., T. Dunning, G. Sutton, M. Adams, J. C. Venter, and C.
+Fields (1993). A quality control algorithm for DNA sequencing
+projects.  Nucleic Acids Research (in press)."
+- from the README file
+
+--
+Tony Maher <tonym@biolateral.com.au>
diff --git a/biology/dna-qc/pkg-plist b/biology/dna-qc/pkg-plist
new file mode 100644
index 000000000000..09192275d6fa
--- /dev/null
+++ b/biology/dna-qc/pkg-plist
@@ -0,0 +1,25 @@
+bin/counter
+bin/hybridize
+bin/normalize
+bin/random_clip
+bin/random_line
+%%PORTDOCS%%share/doc/dna-qc/qc_algorithm.ps.Z
+%%PORTDOCS%%share/doc/dna-qc/qc_fig1.ps.Z
+%%PORTDOCS%%share/doc/dna-qc/qc_fig2a.ps.Z
+%%PORTDOCS%%share/doc/dna-qc/qc_fig2b.ps.Z
+%%PORTDOCS%%share/doc/dna-qc/qc_fig2c.ps.Z
+%%PORTDOCS%%share/doc/dna-qc/qc_fig3.ps.Z
+%%PORTDOCS%%share/doc/dna-qc/qc_fig4.ps.Z
+%%PORTDOCS%%share/doc/dna-qc/qc_fig5.ps.Z
+%%PORTDOCS%%share/doc/dna-qc/qc_fig6.ps.Z
+%%PORTDOCS%%share/doc/dna-qc/qc_fig7.ps.Z
+%%PORTDOCS%%share/doc/dna-qc/surprize.ps.Z
+%%PORTDOCS%%share/examples/dna-qc/README
+%%PORTDOCS%%share/examples/dna-qc/bact.all
+%%PORTDOCS%%share/examples/dna-qc/chromosomeIII.all
+%%PORTDOCS%%share/examples/dna-qc/human.all
+%%PORTDOCS%%share/examples/dna-qc/script.compare
+%%PORTDOCS%%share/examples/dna-qc/script.limits
+%%PORTDOCS%%share/examples/dna-qc/worm.all
+%%PORTDOCS%%@dirrm share/examples/dna-qc
+%%PORTDOCS%%@dirrm share/doc/dna-qc