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authorJohann Visagie <wjv@FreeBSD.org>2001-08-06 14:41:58 +0000
committerJohann Visagie <wjv@FreeBSD.org>2001-08-06 14:41:58 +0000
commitcd0583a2a8734f8b3b456bd12a7ab888bccbfe81 (patch)
tree9fe74ec2576dddd8f6f6405a74e8917f65938983 /biology
parentCorrect my email address. (diff)
Add coalesce 1.50, a program to fit population models.
Notes
Notes: svn path=/head/; revision=45884
Diffstat (limited to 'biology')
-rw-r--r--biology/Makefile1
-rw-r--r--biology/coalesce/Makefile29
-rw-r--r--biology/coalesce/distinfo1
-rw-r--r--biology/coalesce/files/patch-Makefile25
-rw-r--r--biology/coalesce/pkg-comment1
-rw-r--r--biology/coalesce/pkg-descr12
-rw-r--r--biology/coalesce/pkg-plist4
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