diff options
author | Johann Visagie <wjv@FreeBSD.org> | 2001-08-06 14:41:58 +0000 |
---|---|---|
committer | Johann Visagie <wjv@FreeBSD.org> | 2001-08-06 14:41:58 +0000 |
commit | cd0583a2a8734f8b3b456bd12a7ab888bccbfe81 (patch) | |
tree | 9fe74ec2576dddd8f6f6405a74e8917f65938983 /biology | |
parent | Correct 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/Makefile | 1 | ||||
-rw-r--r-- | biology/coalesce/Makefile | 29 | ||||
-rw-r--r-- | biology/coalesce/distinfo | 1 | ||||
-rw-r--r-- | biology/coalesce/files/patch-Makefile | 25 | ||||
-rw-r--r-- | biology/coalesce/pkg-comment | 1 | ||||
-rw-r--r-- | biology/coalesce/pkg-descr | 12 | ||||
-rw-r--r-- | biology/coalesce/pkg-plist | 4 |
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 |