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>

5 files changed, 60 insertions, 0 deletions

diff --git a/biology/Makefile b/biology/Makefile
index 8a93091edb9..37da8a15a1c 100644
--- a/biology/Makefile
+++ b/biology/Makefile
@@ -5,6 +5,7 @@
 
     SUBDIR += L-Breeder
     SUBDIR += act
+    SUBDIR += ariadne
     SUBDIR += artemis
     SUBDIR += avida
     SUBDIR += babel
diff --git a/biology/ariadne/Makefile b/biology/ariadne/Makefile
new file mode 100644
index 00000000000..e477b5a3fd3
--- /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 00000000000..f7ceb435824
--- /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 00000000000..e1df53602fb
--- /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 00000000000..cc92b2c7ea5
--- /dev/null
+++ b/biology/ariadne/pkg-plist
@@ -0,0 +1,4 @@
+bin/ariadne
+bin/prospero
+%%PORTDOCS%%%%DOCSDIR%%/README
+%%PORTDOCS%%@dirrm %%DOCSDIR%%