Initial import of fluctuate, one of the many packages provided by

brook at biology dot nmsu dot edu and his team at NMSU.

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.

6 files changed, 106 insertions, 0 deletions

diff --git a/biology/fluctuate/DESCR b/biology/fluctuate/DESCR
new file mode 100644
index 00000000000..ca4211c0edc
--- /dev/null
+++ b/biology/fluctuate/DESCR
@@ -0,0 +1,5 @@
+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.
diff --git a/biology/fluctuate/MESSAGE b/biology/fluctuate/MESSAGE
new file mode 100644
index 00000000000..9df14f254b0
--- /dev/null
+++ b/biology/fluctuate/MESSAGE
@@ -0,0 +1,9 @@
+===========================================================================
+$NetBSD: MESSAGE,v 1.1.1.1 2003/09/30 01:19:31 jschauma Exp $
+
+In order to run the fluctuate example, you should create a directory for
+example files and then copy ${PREFIX}/share/examples/fluctuate/{bestree,
+infile,outfile} to there.  After that, you can simply run 'fluctuate' from
+that directory.
+
+===========================================================================
diff --git a/biology/fluctuate/Makefile b/biology/fluctuate/Makefile
new file mode 100644
index 00000000000..99c8a1cd405
--- /dev/null
+++ b/biology/fluctuate/Makefile
@@ -0,0 +1,33 @@
+# $NetBSD: Makefile,v 1.1.1.1 2003/09/30 01:19:31 jschauma Exp $
+#
+
+DISTNAME=	fluctuate1.4.src.doc
+PKGNAME=	fluctuate-1.4
+WRKSRC=		${WRKDIR}/fluctuate1.4
+CATEGORIES=	biology
+MASTER_SITES=	ftp://evolution.genetics.washington.edu/pub/lamarc/fluctuate/
+
+MAINTAINER=	brook@nmsu.edu
+HOMEPAGE=	http://evolution.genetics.washington.edu/lamarc/fluctuate.html
+COMMENT=	Estimation of population growth rate
+
+USE_BUILDLINK2=	YES
+ALL_TARGET=	fluctuate
+
+DOCDIR=		${PREFIX}/share/doc/fluctuate
+EXDIR=		${PREFIX}/share/examples/fluctuate
+DOCFILES=	fluctuate.doc errors.doc
+EXFILES=	bestree infile outfile
+
+do-install:
+	${INSTALL_PROGRAM} ${WRKSRC}/fluctuate ${PREFIX}/bin/
+	${INSTALL_DATA_DIR} ${DOCDIR}
+	${INSTALL_DATA_DIR} ${EXDIR}
+	for f in ${DOCFILES}; do 				\
+		${INSTALL_DATA} ${WRKSRC}/$$f ${DOCDIR}/$$f; 	\
+	done
+	for f in ${EXFILES}; do 				\
+		${INSTALL_DATA} ${WRKSRC}/$$f ${EXDIR}/$$f; 	\
+	done
+
+.include "../../mk/bsd.pkg.mk"
diff --git a/biology/fluctuate/PLIST b/biology/fluctuate/PLIST
new file mode 100644
index 00000000000..66ae75d4508
--- /dev/null
+++ b/biology/fluctuate/PLIST
@@ -0,0 +1,9 @@
+@comment $NetBSD: PLIST,v 1.1.1.1 2003/09/30 01:19:31 jschauma Exp $
+bin/fluctuate
+share/doc/fluctuate/errors.doc
+share/doc/fluctuate/fluctuate.doc
+share/examples/fluctuate/bestree
+share/examples/fluctuate/infile
+share/examples/fluctuate/outfile
+@dirrm share/examples/fluctuate
+@dirrm share/doc/fluctuate
diff --git a/biology/fluctuate/distinfo b/biology/fluctuate/distinfo
new file mode 100644
index 00000000000..eb05ed6d21b
--- /dev/null
+++ b/biology/fluctuate/distinfo
@@ -0,0 +1,5 @@
+$NetBSD: distinfo,v 1.1.1.1 2003/09/30 01:19:31 jschauma Exp $
+
+SHA1 (fluctuate1.4.src.doc.tar.gz) = 7e9fb766312237f85a191327aae37c9a52a2e408
+Size (fluctuate1.4.src.doc.tar.gz) = 70690 bytes
+SHA1 (patch-aa) = d7637d2d2b47d9ceb920319393f13e84a60bfae0
diff --git a/biology/fluctuate/patches/patch-aa b/biology/fluctuate/patches/patch-aa
new file mode 100644
index 00000000000..65ad09b6be9
--- /dev/null
+++ b/biology/fluctuate/patches/patch-aa
@@ -0,0 +1,45 @@
+$NetBSD: patch-aa,v 1.1.1.1 2003/09/30 01:19:32 jschauma Exp $
+
+--- Makefile.orig	2003-09-29 21:08:30.000000000 -0400
++++ Makefile	2003-09-29 21:09:31.000000000 -0400
+@@ -1,30 +1,30 @@
+ LIBS    = -lm
+ BINDIR  = ./bin
+-CFLAGS  = -O2 -funroll-loops 
+-CC        = gcc $(CFLAGS)
++CFLAGS  += -O2 -funroll-loops 
++#CC        = gcc $(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 \
+-    coal_modellike.o $(LIBS) -o fluctuate
++	$(CC) ${CFLAGS} fluctuate.o fluc_modellike.o getdata.o plot.o wrap.o \
++    coal_modellike.o ${LDFLAGS} $(LIBS) -o fluctuate
+ 
+ clean :
+ 	rm fluctuate.o fluc_modellike.o coal_modellike.o getdata.o plot.o wrap.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