diff options
author | Johann Visagie <wjv@FreeBSD.org> | 2001-08-06 14:45:39 +0000 |
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committer | Johann Visagie <wjv@FreeBSD.org> | 2001-08-06 14:45:39 +0000 |
commit | 52619bca7a2acada3959062718cfbb11333d5d57 (patch) | |
tree | bef0bb32746cc0885e64ecdb421e552f88627934 /biology | |
parent | Add coalesce 1.50, a program to fit population models. (diff) |
Add fluctuate 1.30, a program to fit population models.
Notes
Notes:
svn path=/head/; revision=45885
Diffstat (limited to 'biology')
-rw-r--r-- | biology/Makefile | 1 | ||||
-rw-r--r-- | biology/fluctuate/Makefile | 29 | ||||
-rw-r--r-- | biology/fluctuate/distinfo | 1 | ||||
-rw-r--r-- | biology/fluctuate/files/patch-Makefile | 40 | ||||
-rw-r--r-- | biology/fluctuate/pkg-comment | 1 | ||||
-rw-r--r-- | biology/fluctuate/pkg-descr | 13 | ||||
-rw-r--r-- | biology/fluctuate/pkg-plist | 4 |
7 files changed, 89 insertions, 0 deletions
diff --git a/biology/Makefile b/biology/Makefile index 7a6c444d92d3..7a5c0de1f614 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -11,6 +11,7 @@ SUBDIR += fasta SUBDIR += fasta3 SUBDIR += fastdnaml + SUBDIR += fluctuate SUBDIR += gaussian98 SUBDIR += genpak SUBDIR += gperiodic diff --git a/biology/fluctuate/Makefile b/biology/fluctuate/Makefile new file mode 100644 index 000000000000..551298c13b85 --- /dev/null +++ b/biology/fluctuate/Makefile @@ -0,0 +1,29 @@ +# New ports collection makefile for: fluctuate +# Date created: 6 August 2001 +# Whom: Johann Visagie <wjv@FreeBSD.org> +# +# $FreeBSD$ +# + +PORTNAME= fluctuate +PORTVERSION= 1.30 +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/fluctuate/distinfo b/biology/fluctuate/distinfo new file mode 100644 index 000000000000..36ce138d8b10 --- /dev/null +++ b/biology/fluctuate/distinfo @@ -0,0 +1 @@ +MD5 (fluctuate.tar.Z) = 86619e6885fdf172b39dd8a7eb814bba diff --git a/biology/fluctuate/files/patch-Makefile b/biology/fluctuate/files/patch-Makefile new file mode 100644 index 000000000000..186784a3e2c5 --- /dev/null +++ b/biology/fluctuate/files/patch-Makefile @@ -0,0 +1,40 @@ +--- Makefile.orig Thu Sep 3 00:56:03 1998 ++++ Makefile Mon Aug 6 15:58:49 2001 +@@ -1,30 +1,28 @@ + LIBS = -lm + BINDIR = ./bin +-CFLAGS = -O +-CC = cc $(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 \ ++ $(CC) $(CFLAGS) fluctuate.o fluc_modellike.o getdata.o plot.o wrap.o \ + coal_modellike.o $(LIBS) -o fluctuate + + clean : + rm fluctuate.o fluc_modellike.o coal_modellike.o getdata.o plot.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 diff --git a/biology/fluctuate/pkg-comment b/biology/fluctuate/pkg-comment new file mode 100644 index 000000000000..8e9f159f703c --- /dev/null +++ b/biology/fluctuate/pkg-comment @@ -0,0 +1 @@ +A program to fit population models diff --git a/biology/fluctuate/pkg-descr b/biology/fluctuate/pkg-descr new file mode 100644 index 000000000000..1198938d1d95 --- /dev/null +++ b/biology/fluctuate/pkg-descr @@ -0,0 +1,13 @@ +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. + +Fluctuate 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/fluctuate.html + +-- Johann Visagie <wjv@FreeBSD.org> diff --git a/biology/fluctuate/pkg-plist b/biology/fluctuate/pkg-plist new file mode 100644 index 000000000000..6aed79770140 --- /dev/null +++ b/biology/fluctuate/pkg-plist @@ -0,0 +1,4 @@ +bin/fluctuate +%%PORTDOCS%%share/doc/fluctuate/errors.doc +%%PORTDOCS%%share/doc/fluctuate/fluctuate.doc +%%PORTDOCS%%@dirrm share/doc/fluctuate |