diff options
author | Johann Visagie <wjv@FreeBSD.org> | 2001-08-06 14:49:53 +0000 |
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committer | Johann Visagie <wjv@FreeBSD.org> | 2001-08-06 14:49:53 +0000 |
commit | 043c249d98e3cecabda732fe063ff7efc496d6f0 (patch) | |
tree | 3f4903a31df7082a3ffa7b1423fadfac8fff2fd2 /biology | |
parent | Add fluctuate 1.30, a program to fit population models. (diff) |
Add recombine 1.40, a program to fit population models across sites.
Notes
Notes:
svn path=/head/; revision=45886
Diffstat (limited to 'biology')
-rw-r--r-- | biology/Makefile | 1 | ||||
-rw-r--r-- | biology/recombine/Makefile | 29 | ||||
-rw-r--r-- | biology/recombine/distinfo | 1 | ||||
-rw-r--r-- | biology/recombine/files/patch-Makefile | 117 | ||||
-rw-r--r-- | biology/recombine/pkg-comment | 1 | ||||
-rw-r--r-- | biology/recombine/pkg-descr | 12 | ||||
-rw-r--r-- | biology/recombine/pkg-plist | 5 |
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 |