From bd7a90118c9c14cb0ec41c88db6445bfdbf3ea06 Mon Sep 17 00:00:00 2001
From: Kirill Ponomarev <krion@FreeBSD.org>
Date: Tue, 22 Jun 2004 14:29:59 +0000
Subject: Add ariadne 1.3, programs to compare protein sequences and profiles,
 using the Smith-Waterman algorithm.

PR:		ports/67811
Submitted by:	Fernan Aguero <fernan@iib.unsam.edu.ar>
---
 biology/ariadne/Makefile  | 35 +++++++++++++++++++++++++++++++++++
 biology/ariadne/distinfo  |  2 ++
 biology/ariadne/pkg-descr | 18 ++++++++++++++++++
 biology/ariadne/pkg-plist |  4 ++++
 4 files changed, 59 insertions(+)
 create mode 100644 biology/ariadne/Makefile
 create mode 100644 biology/ariadne/distinfo
 create mode 100644 biology/ariadne/pkg-descr
 create mode 100644 biology/ariadne/pkg-plist

(limited to 'biology/ariadne')

diff --git a/biology/ariadne/Makefile b/biology/ariadne/Makefile
new file mode 100644
index 000000000000..e477b5a3fd31
--- /dev/null
+++ b/biology/ariadne/Makefile
@@ -0,0 +1,35 @@
+# New ports collection makefile for:	ariadne
+# Date created:		10 Jun 2004
+# Whom:	      		Fernan Aguero <fernan@iib.unsam.edu.ar>
+#
+# $FreeBSD$
+#
+
+PORTNAME=	ariadne
+PORTVERSION=	1.3
+CATEGORIES=	biology
+MASTER_SITES=	http://www.well.ox.ac.uk/ariadne/
+EXTRACT_SUFX=	.tar.Z
+
+MAINTAINER=	fernan@iib.unsam.edu.ar
+COMMENT=	Programs to compare protein sequences and profiles
+
+WRKSRC=		${WRKDIR}/SRC-${PORTVERSION}
+USE_GMAKE=	yes
+USE_REINPLACE=	yes
+
+post-patch:
+	@${REINPLACE_CMD} -e 's|-lpthread|${PTHREAD_LIBS}| ; \
+		s|CC =|CC ?=| ; \
+		s|CFLAGS =|CFLAGS +=| ; \
+		s|-c $(OPTIMISE)|-c $(CFLAGS) $(OPTIMIZE)|g' ${WRKSRC}/Makefile
+
+do-install:
+	${INSTALL_PROGRAM} ${WRKSRC}/${OPSYS}/ariadne ${PREFIX}/bin
+	${INSTALL_PROGRAM} ${WRKSRC}/${OPSYS}/prospero ${PREFIX}/bin
+.if !defined(NOPORTDOCS)
+	@${MKDIR} ${DOCSDIR}
+	${INSTALL_DATA} ${WRKSRC}/README ${DOCSDIR}
+.endif
+
+.include <bsd.port.mk>
diff --git a/biology/ariadne/distinfo b/biology/ariadne/distinfo
new file mode 100644
index 000000000000..f7ceb4358242
--- /dev/null
+++ b/biology/ariadne/distinfo
@@ -0,0 +1,2 @@
+MD5 (ariadne-1.3.tar.Z) = 240dc8b278a02b0fcdf56cd186d9b0ec
+SIZE (ariadne-1.3.tar.Z) = 69427
diff --git a/biology/ariadne/pkg-descr b/biology/ariadne/pkg-descr
new file mode 100644
index 000000000000..e1df53602fbf
--- /dev/null
+++ b/biology/ariadne/pkg-descr
@@ -0,0 +1,18 @@
+ARIADNE is a package of two programs, ariadne and prospero, that compare
+protein sequences and profiles using the Smith-Waterman algorithm, and
+assesses statistical significance using a new accurate formula,
+described in Mott, 2000, "Accurate Formula for P-values of gapped local
+sequence and profile alignments" J. Mol Biol. 300:649-659.
+
+The sequence/profile comparison algorithms used in ARIADNE are standard,
+and are probably not the fastest implementations available. The novel
+part is the method for determining statistical significance, which will
+give thresholds of significance that are accurate to within 5% 95% of
+the time.
+
+The package is written in ANSI C. You are free to incorporate the method
+used for assessing statistical significance into third-party code,
+provided you cite the above reference. The routines for assessing
+significance are all in gaplib.c 
+
+WWW: http://www.well.ox.ac.uk/ariadne/
diff --git a/biology/ariadne/pkg-plist b/biology/ariadne/pkg-plist
new file mode 100644
index 000000000000..cc92b2c7ea50
--- /dev/null
+++ b/biology/ariadne/pkg-plist
@@ -0,0 +1,4 @@
+bin/ariadne
+bin/prospero
+%%PORTDOCS%%%%DOCSDIR%%/README
+%%PORTDOCS%%@dirrm %%DOCSDIR%%
-- 
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