Add fluctuate 1.30, a program to fit population models.

7 files changed, 89 insertions, 0 deletions

diff --git a/biology/Makefile b/biology/Makefile
index 7a6c444..7a5c0de 100644
--- a/biology/Makefile
+++ b/biology/Makefile
@@ -11,6 +11,7 @@
     SUBDIR += fasta
     SUBDIR += fasta3
     SUBDIR += fastdnaml
+    SUBDIR += fluctuate
     SUBDIR += gaussian98
     SUBDIR += genpak
     SUBDIR += gperiodic
diff --git a/biology/fluctuate/Makefile b/biology/fluctuate/Makefile
new file mode 100644
index 0000000..551298c
--- /dev/null
+++ b/biology/fluctuate/Makefile
@@ -0,0 +1,29 @@
+# New ports collection makefile for:	fluctuate
+# Date created:		6 August 2001
+# Whom:	      		Johann Visagie <wjv@FreeBSD.org>
+#
+# $FreeBSD$
+#
+
+PORTNAME=	fluctuate
+PORTVERSION=	1.30
+CATEGORIES=	biology
+MASTER_SITES=	ftp://evolution.genetics.washington.edu/pub/lamarc/
+DISTNAME=	${PORTNAME}
+EXTRACT_SUFX=	.tar.Z
+
+MAINTAINER=	wjv@FreeBSD.org
+
+NO_WRKSUBDIR=	yes
+ALL_TARGET=	${PORTNAME}
+
+do-install:
+	@ ${INSTALL_PROGRAM} ${WRKSRC}/${PORTNAME} ${PREFIX}/bin/
+
+post-install:
+.if !defined(NOPORTDOCS)
+	@ ${MKDIR} ${DOCSDIR}
+	@ ${INSTALL_DATA} ${WRKSRC}/*.doc ${DOCSDIR}/
+.endif
+
+.include <bsd.port.mk>
diff --git a/biology/fluctuate/distinfo b/biology/fluctuate/distinfo
new file mode 100644
index 0000000..36ce138
--- /dev/null
+++ b/biology/fluctuate/distinfo
@@ -0,0 +1 @@
+MD5 (fluctuate.tar.Z) = 86619e6885fdf172b39dd8a7eb814bba
diff --git a/biology/fluctuate/files/patch-Makefile b/biology/fluctuate/files/patch-Makefile
new file mode 100644
index 0000000..186784a
--- /dev/null
+++ b/biology/fluctuate/files/patch-Makefile
@@ -0,0 +1,40 @@
+--- Makefile.orig	Thu Sep  3 00:56:03 1998
++++ Makefile	Mon Aug  6 15:58:49 2001
+@@ -1,30 +1,28 @@
+ LIBS    = -lm
+ BINDIR  = ./bin
+-CFLAGS  = -O
+-CC        = cc $(CFLAGS)
+ 
+ fluctuate : fluctuate.o fluc_modellike.o getdata.o plot.o wrap.o \
+     coal_modellike.o
+-	$(CC) fluctuate.o fluc_modellike.o getdata.o plot.o wrap.o \
++	$(CC) $(CFLAGS) fluctuate.o fluc_modellike.o getdata.o plot.o wrap.o \
+     coal_modellike.o $(LIBS) -o fluctuate
+ 
+ clean : 
+ 	rm fluctuate.o fluc_modellike.o coal_modellike.o getdata.o plot.o 
+ 
+ fluctuate.o : fluctuate.c
+-	$(CC) -c fluctuate.c
++	$(CC) $(CFLAGS) -c fluctuate.c
+ 
+ fluc_modellike.o : fluc_modellike.c
+-	$(CC) -c fluc_modellike.c
++	$(CC) $(CFLAGS) -c fluc_modellike.c
+ 
+ coal_modellike.o : coal_modellike.c
+-	$(CC) -c coal_modellike.c
++	$(CC) $(CFLAGS) -c coal_modellike.c
+ 
+ getdata.o : getdata.c
+-	$(CC) -c getdata.c
++	$(CC) $(CFLAGS) -c getdata.c
+ 
+ plot.o : plot.c
+-	$(CC) -c plot.c
++	$(CC) $(CFLAGS) -c plot.c
+ 
+ wrap.o : wrap.c
+-	$(CC) -c wrap.c
++	$(CC) $(CFLAGS) -c wrap.c
diff --git a/biology/fluctuate/pkg-comment b/biology/fluctuate/pkg-comment
new file mode 100644
index 0000000..8e9f159
--- /dev/null
+++ b/biology/fluctuate/pkg-comment
@@ -0,0 +1 @@
+A program to fit population models
diff --git a/biology/fluctuate/pkg-descr b/biology/fluctuate/pkg-descr
new file mode 100644
index 0000000..1198938
--- /dev/null
+++ b/biology/fluctuate/pkg-descr
@@ -0,0 +1,13 @@
+Fluctuate fits the model which has a single population which has been growing
+(or shrinking) according to an exponential growth law.  It estimates 4Nu and
+g, where N is the effective population size, u is the neutral mutation rate
+per site, and g is the growth rate of the population.
+
+Fluctuate forms part of the Lamarc (Likelihood Analysis with Metropolis
+Algorithm using Random Coalescence) suite.  See:
+
+  http://evolution.genetics.washington.edu/lamarc.html
+
+WWW:    http://evolution.genetics.washington.edu/lamarc/fluctuate.html
+
+-- Johann Visagie <wjv@FreeBSD.org>
diff --git a/biology/fluctuate/pkg-plist b/biology/fluctuate/pkg-plist
new file mode 100644
index 0000000..6aed797
--- /dev/null
+++ b/biology/fluctuate/pkg-plist
@@ -0,0 +1,4 @@
+bin/fluctuate
+%%PORTDOCS%%share/doc/fluctuate/errors.doc
+%%PORTDOCS%%share/doc/fluctuate/fluctuate.doc
+%%PORTDOCS%%@dirrm share/doc/fluctuate