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

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

COALESCE fits the model which has a single population of constant size, and
estimates 4Nu, where N is the effective population size and u is the neutral
mutation rate per site.

5 files changed, 85 insertions, 0 deletions

diff --git a/biology/coalesce/DESCR b/biology/coalesce/DESCR
new file mode 100644
index 00000000000..d788c25411e
--- /dev/null
+++ b/biology/coalesce/DESCR
@@ -0,0 +1,3 @@
+COALESCE fits the model which has a single population of constant size, and
+estimates 4Nu, where N is the effective population size and u is the neutral
+mutation rate per site.
diff --git a/biology/coalesce/Makefile b/biology/coalesce/Makefile
new file mode 100644
index 00000000000..1c46cde2dd1
--- /dev/null
+++ b/biology/coalesce/Makefile
@@ -0,0 +1,33 @@
+# $NetBSD: Makefile,v 1.1.1.1 2003/09/30 01:03:56 jschauma Exp $
+#
+
+DISTNAME=	coalesce1.5b
+PKGNAME=	coalesce-1.5.0.2
+WRKSRC=		${WRKDIR}/coalesce1.5beta
+CATEGORIES=	biology
+MASTER_SITES=	ftp://evolution.genetics.washington.edu/pub/lamarc/coalesce/
+
+MAINTAINER=	brook@nmsu.edu
+HOMEPAGE=	http://evolution.genetics.washington.edu/lamarc/coalesce.html
+COMMENT=	Estimates effective population size and mutation rate
+
+USE_BUILDLINK2=	YES
+ALL_TARGET=	coalesce
+
+DOCDIR=		${PREFIX}/share/doc/coalesce
+EXDIR=		${PREFIX}/share/examples/coalesce
+DOCFILES=	coalesce.doc errors.doc readme
+EXFILES=	bestree infile intree outfile parmfile seedfile
+
+do-install:
+	${INSTALL_DATA_DIR} ${DOCDIR}
+	${INSTALL_DATA_DIR} ${EXDIR}
+	${INSTALL_PROGRAM} ${WRKSRC}/coalesce ${PREFIX}/bin/
+	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/coalesce/PLIST b/biology/coalesce/PLIST
new file mode 100644
index 00000000000..0ff8c903eaa
--- /dev/null
+++ b/biology/coalesce/PLIST
@@ -0,0 +1,13 @@
+@comment $NetBSD: PLIST,v 1.1.1.1 2003/09/30 01:03:56 jschauma Exp $
+bin/coalesce
+share/doc/coalesce/coalesce.doc
+share/doc/coalesce/errors.doc
+share/doc/coalesce/readme
+share/examples/coalesce/bestree
+share/examples/coalesce/infile
+share/examples/coalesce/intree
+share/examples/coalesce/outfile
+share/examples/coalesce/parmfile
+share/examples/coalesce/seedfile
+@dirrm share/examples/coalesce
+@dirrm share/doc/coalesce
diff --git a/biology/coalesce/distinfo b/biology/coalesce/distinfo
new file mode 100644
index 00000000000..5119f699c09
--- /dev/null
+++ b/biology/coalesce/distinfo
@@ -0,0 +1,5 @@
+$NetBSD: distinfo,v 1.1.1.1 2003/09/30 01:03:56 jschauma Exp $
+
+SHA1 (coalesce1.5b.tar.gz) = ec2a13da25474440a0c57b2a2e634c94db30961e
+Size (coalesce1.5b.tar.gz) = 46153 bytes
+SHA1 (patch-aa) = b4c3afcb563c54d4b16f20f8b4b9fc649b49deee
diff --git a/biology/coalesce/patches/patch-aa b/biology/coalesce/patches/patch-aa
new file mode 100644
index 00000000000..fcc1df0d663
--- /dev/null
+++ b/biology/coalesce/patches/patch-aa
@@ -0,0 +1,31 @@
+$NetBSD: patch-aa,v 1.1.1.1 2003/09/30 01:03:56 jschauma Exp $
+
+--- Makefile.orig	1996-02-29 11:00:09.000000000 -0500
++++ Makefile	2003-09-29 20:51:32.000000000 -0400
+@@ -1,20 +1,20 @@
+ LIBS    = -lm
+ BINDIR  = ./bin
+-CFLAGS  = -g
+-CC        = cc $(CFLAGS)
++#CFLAGS  = -g
++#CC        = cc $(CFLAGS)
+ DCC     = gcc -g -DDMALLOC_FUNC_CHECK -ansi -pedantic
+ DLIBS   = -lm -L/usr/local/lib -ldmalloc
+ # -O
+ PROGS   =          coalesce fluctuate
+ 
+ coalesce :  coalesce.c constants.h lamarc.h
+-	$(CC) coalesce.c $(LIBS) -o coalesce
++	$(CC) ${CFLAGS} coalesce.c ${LDFLAGS} $(LIBS) -o coalesce
+ 
+ modellike.o : modellike.c
+-	$(CC) -c modellike.c
++	$(CC) ${CFLAGS} -c modellike.c
+ 
+ fluctuate.o : fluctuate.c
+-	$(CC) -c fluctuate.c
++	$(CC) ${CFLAGS} -c fluctuate.c
+ 
+ fluctuate : fluctuate.o modellike.o
+-	$(CC) fluctuate.o modellike.o $(LIBS) -o fluctuate
++	$(CC) ${CFLAGS} fluctuate.o modellike.o ${LDFLAGS} $(LIBS) -o fluctuate