Add recombine 1.40, a program to fit population models across sites.

7 files changed, 166 insertions, 0 deletions

diff --git a/biology/Makefile b/biology/Makefile
index 7a5c0de1f614..9219419b5a96 100644
--- a/biology/Makefile
+++ b/biology/Makefile
@@ -33,6 +33,7 @@
     SUBDIR += psi88
     SUBDIR += py-biopython
     SUBDIR += rasmol
+    SUBDIR += recombine
     SUBDIR += seaview
     SUBDIR += sim4
     SUBDIR += tinker
diff --git a/biology/recombine/Makefile b/biology/recombine/Makefile
new file mode 100644
index 000000000000..51e89b10632f
--- /dev/null
+++ b/biology/recombine/Makefile
@@ -0,0 +1,29 @@
+# New ports collection makefile for:	recombine
+# Date created:		6 August 2001
+# Whom:	      		Johann Visagie <wjv@FreeBSD.org>
+#
+# $FreeBSD$
+#
+
+PORTNAME=	recombine
+PORTVERSION=	1.40
+CATEGORIES=	biology
+MASTER_SITES=	ftp://evolution.genetics.washington.edu/pub/lamarc/recombine/
+DISTNAME=	${PORTNAME}${PORTVERSION}
+
+MAINTAINER=	wjv@FreeBSD.org
+
+NO_WRKSUBDIR=	yes
+ALL_TARGET=	${PORTNAME}
+
+do-install:
+	@ ${INSTALL_PROGRAM} ${WRKSRC}/${PORTNAME} ${PREFIX}/bin/
+	@ ${INSTALL_SCRIPT} ${WRKSRC}/filetran ${PREFIX}/bin/
+
+post-install:
+.if !defined(NOPORTDOCS)
+	@ ${MKDIR} ${DOCSDIR}
+	@ ${INSTALL_DATA} ${WRKSRC}/*.doc ${DOCSDIR}/
+.endif
+
+.include <bsd.port.mk>
diff --git a/biology/recombine/distinfo b/biology/recombine/distinfo
new file mode 100644
index 000000000000..59704511dc47
--- /dev/null
+++ b/biology/recombine/distinfo
@@ -0,0 +1 @@
+MD5 (recombine1.40.tar.gz) = 78f308f69c35610fbd31a091b8d17e2f
diff --git a/biology/recombine/files/patch-Makefile b/biology/recombine/files/patch-Makefile
new file mode 100644
index 000000000000..de759e7d7bf9
--- /dev/null
+++ b/biology/recombine/files/patch-Makefile
@@ -0,0 +1,117 @@
+--- Makefile.orig	Wed Oct 25 23:39:34 2000
++++ Makefile	Mon Aug  6 16:13:02 2001
+@@ -1,105 +1,37 @@
+ LIBS    = -lm
+ BINDIR  = ./bin
+-#CFLAGS  = -Wall -Wshadow -g
+-CFLAGS  = -O -Wall -Wshadow -g
+-#CFLAGS  = -fast -inline speed
+-#CFLAGS  = -O3 -arch host -fast
+-CC        = gcc $(CFLAGS)
+-#CC        = cc $(CFLAGS)
++CFLAGS += -g
+ DCC     = gcc -g -Wall -DDMALLOC_FUNC_CHECK -ansi -pedantic
+ PLUSCC    = g++ $(CFLAGS)
+ LIBS   = -lm -L/usr/local/lib
+ DLIBS   = -lm -L/usr/local/lib -ldmalloc
+ CGCC    = checkergcc -g -Wall
+ CGLIBS  = -lm
+-# -O
+ PROGS   =           recombine
+ 
+ # The big banana
+ recombine : recombine.o jdrop.o rec_modellike.o jworld.o getdata.o \
+ 	traitlike.o getmsatdata.o
+-	$(CC) -o recombine recombine.o jdrop.o rec_modellike.o \
++	$(CC) $(CFLAGS) -o recombine recombine.o jdrop.o rec_modellike.o \
+ 	jworld.o getdata.o traitlike.o getmsatdata.o $(LIBS)
+ 
+ jworld.o : jworld.c
+-	$(CC) -c jworld.c
++	$(CC) $(CFLAGS) -c jworld.c
+ 
+ jdrop.o : jdrop.c
+-	$(CC) -c jdrop.c
++	$(CC) $(CFLAGS) -c jdrop.c
+ 
+ rec_modellike.o : rec_modellike.c
+-	$(CC) -c rec_modellike.c
++	$(CC) $(CFLAGS) -c rec_modellike.c
+ 
+ recombine.o : recombine.c
+-	$(CC) -c recombine.c 
++	$(CC) $(CFLAGS) -c recombine.c 
+ 
+ getdata.o : getdata.c
+-	$(CC) -c getdata.c
++	$(CC) $(CFLAGS) -c getdata.c
+ 
+ getmsatdata.o : getmsatdata.c
+-	$(CC) -c getmsatdata.c
++	$(CC) $(CFLAGS) -c getmsatdata.c
+ 
+ traitlike.o : traitlike.c
+-	$(CC) -c traitlike.c
+-
+-rectreedna : rectreedna.c
+-	$(CC) -o rectreedna rectreedna.c $(LIBS)
+-
+-hapdna : hapdna.c
+-	$(CC) -o hapdna hapdna.c $(LIBS)
+-
+-mhapdna : mhapdna.c
+-	$(CC) -o mhapdna mhapdna.c $(LIBS)
+-
+-drecombine.o : recombine.c
+-	$(CC) -o drecombine.o -c recombine.c
+-
+-djdrop.o : jdrop.c
+-	$(CC)  -o djdrop.o -c jdrop.c
+-
+-drec_modellike.o : rec_modellike.c
+-	$(CC) -o drec_modellike.o -c rec_modellike.c
+-
+-djworld.o : jworld.c
+-	$(CC) -o djworld.o -c jworld.c
+-
+-dgetdata.o : getdata.c
+-	$(CC) -o dgetdata.o -c getdata.c
+-
+-dgetmsatdata.o : getmsatdata.c
+-	$(CC) -o dgetmsatdata.o -c getmsatdata.c
+-
+-drecombine:  drecombine.o djdrop.o drec_modellike.o djworld.o dgetdata.o memdebug.o memalpha.o memfree.o \
+-        dgetmsatdata.o
+-	$(CC) drecombine.o djdrop.o drec_modellike.o djworld.o dgetdata.o memdebug.o memalpha.o memfree.o \
+-	dgetmsatdata.o $(LIBS) -o drecombine
+-
+-dclean: 
+-	rm drecombine.o djdrop.o drec_modellike.o djworld.o dgetdata.o dgetmsatdata.o
+-
+-clean :
+-	rm -f *.o
+-
+-gentrees.o : gentrees.c
+-	$(CC) -c gentrees.c
+-
+-segtre_mig.o : segtre_mig.c
+-	$(CC) -c segtre_mig.c
+-
+-rectree : gentrees.o segtre_mig.o
+-	$(CC) gentrees.o segtre_mig.o $(LIBS) -o rectree
+-
+-jrectree : simrectree.c
+-	$(CC) simrectree.c $(LIBS) -o jrectree
+-
+-snp : snp.c
+-	$(CC) snp.c $(LIBS) -o snp
+-
+-panelmaker : panelmaker.c
+-	$(CC) panelmaker.c $(LIBS) -o panelmaker
+-
+-variance : variance.c
+-	$(CC) variance.c $(LIBS) -o variance
+-
+-distree : distree.c
+-	$(CC) distree.c $(LIBS) -o distree
++	$(CC) $(CFLAGS) -c traitlike.c
diff --git a/biology/recombine/pkg-comment b/biology/recombine/pkg-comment
new file mode 100644
index 000000000000..00509aa636c0
--- /dev/null
+++ b/biology/recombine/pkg-comment
@@ -0,0 +1 @@
+A program to fit population models across sites
diff --git a/biology/recombine/pkg-descr b/biology/recombine/pkg-descr
new file mode 100644
index 000000000000..f6af628d2837
--- /dev/null
+++ b/biology/recombine/pkg-descr
@@ -0,0 +1,12 @@
+Recombine fits a model which has a single population of constant size with a
+single recombination rate across all sites.  It can accomodate either plain
+DNA or RNA data or SNP (single nucleotide polymorphism) data.
+
+Recombine 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/recombine/pkg-plist b/biology/recombine/pkg-plist
new file mode 100644
index 000000000000..8c01fcc4b69c
--- /dev/null
+++ b/biology/recombine/pkg-plist
@@ -0,0 +1,5 @@
+bin/filetran
+bin/recombine
+%%PORTDOCS%%share/doc/recombine/rec_errors.doc
+%%PORTDOCS%%share/doc/recombine/recombine.doc
+%%PORTDOCS%%@dirrm share/doc/recombine