Add coalesce 1.50, a program to fit population models.

7 files changed, 73 insertions, 0 deletions

diff --git a/biology/Makefile b/biology/Makefile
index d5e3377fe257..7a6c444d92d3 100644
--- a/biology/Makefile
+++ b/biology/Makefile
@@ -5,6 +5,7 @@
     SUBDIR += biojava
     SUBDIR += chemeq
     SUBDIR += clustalw
+    SUBDIR += coalesce
     SUBDIR += deft
     SUBDIR += emboss
     SUBDIR += fasta
diff --git a/biology/coalesce/Makefile b/biology/coalesce/Makefile
new file mode 100644
index 000000000000..7dd0ff4bdbc0
--- /dev/null
+++ b/biology/coalesce/Makefile
@@ -0,0 +1,29 @@
+# New ports collection makefile for:	coalesce
+# Date created:		6 August 2001
+# Whom:	      		Johann Visagie <wjv@FreeBSD.org>
+#
+# $FreeBSD$
+#
+
+PORTNAME=	coalesce
+PORTVERSION=	1.50
+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/coalesce/distinfo b/biology/coalesce/distinfo
new file mode 100644
index 000000000000..2c85e177d50d
--- /dev/null
+++ b/biology/coalesce/distinfo
@@ -0,0 +1 @@
+MD5 (coalesce.tar.Z) = feea2925ac514e644c53c27c497f4081
diff --git a/biology/coalesce/files/patch-Makefile b/biology/coalesce/files/patch-Makefile
new file mode 100644
index 000000000000..ca16d8fbea20
--- /dev/null
+++ b/biology/coalesce/files/patch-Makefile
@@ -0,0 +1,25 @@
+--- Makefile.orig	Thu Feb 29 18:00:09 1996
++++ Makefile	Mon Aug  6 16:32:10 2001
+@@ -1,20 +1,9 @@
+ LIBS    = -lm
+ BINDIR  = ./bin
+-CFLAGS  = -g
+-CC        = cc $(CFLAGS)
++CFLAGS += -g
+ 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
+-
+-modellike.o : modellike.c
+-	$(CC) -c modellike.c
+-
+-fluctuate.o : fluctuate.c
+-	$(CC) -c fluctuate.c
+-
+-fluctuate : fluctuate.o modellike.o
+-	$(CC) fluctuate.o modellike.o $(LIBS) -o fluctuate
++	$(CC) $(CFLAGS) coalesce.c $(LIBS) -o coalesce
diff --git a/biology/coalesce/pkg-comment b/biology/coalesce/pkg-comment
new file mode 100644
index 000000000000..8e9f159f703c
--- /dev/null
+++ b/biology/coalesce/pkg-comment
@@ -0,0 +1 @@
+A program to fit population models
diff --git a/biology/coalesce/pkg-descr b/biology/coalesce/pkg-descr
new file mode 100644
index 000000000000..42961b73dd85
--- /dev/null
+++ b/biology/coalesce/pkg-descr
@@ -0,0 +1,12 @@
+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
+
+Coalesce 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/recombine.html
+
+-- Johann Visagie <wjv@FreeBSD.org>
diff --git a/biology/coalesce/pkg-plist b/biology/coalesce/pkg-plist
new file mode 100644
index 000000000000..4f63eb5abe2d
--- /dev/null
+++ b/biology/coalesce/pkg-plist
@@ -0,0 +1,4 @@
+bin/coalesce
+%%PORTDOCS%%share/doc/coalesce/coalesce.doc
+%%PORTDOCS%%share/doc/coalesce/errors.doc
+%%PORTDOCS%%@dirrm share/doc/coalesce