diff options
Diffstat (limited to 'biology')
-rw-r--r-- | biology/coalesce/DESCR | 3 | ||||
-rw-r--r-- | biology/coalesce/Makefile | 33 | ||||
-rw-r--r-- | biology/coalesce/PLIST | 13 | ||||
-rw-r--r-- | biology/coalesce/distinfo | 5 | ||||
-rw-r--r-- | biology/coalesce/patches/patch-aa | 31 |
5 files changed, 85 insertions, 0 deletions
diff --git a/biology/coalesce/DESCR b/biology/coalesce/DESCR new file mode 100644 index 00000000000..d788c25411e --- /dev/null +++ b/biology/coalesce/DESCR @@ -0,0 +1,3 @@ +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. diff --git a/biology/coalesce/Makefile b/biology/coalesce/Makefile new file mode 100644 index 00000000000..1c46cde2dd1 --- /dev/null +++ b/biology/coalesce/Makefile @@ -0,0 +1,33 @@ +# $NetBSD: Makefile,v 1.1.1.1 2003/09/30 01:03:56 jschauma Exp $ +# + +DISTNAME= coalesce1.5b +PKGNAME= coalesce-1.5.0.2 +WRKSRC= ${WRKDIR}/coalesce1.5beta +CATEGORIES= biology +MASTER_SITES= ftp://evolution.genetics.washington.edu/pub/lamarc/coalesce/ + +MAINTAINER= brook@nmsu.edu +HOMEPAGE= http://evolution.genetics.washington.edu/lamarc/coalesce.html +COMMENT= Estimates effective population size and mutation rate + +USE_BUILDLINK2= YES +ALL_TARGET= coalesce + +DOCDIR= ${PREFIX}/share/doc/coalesce +EXDIR= ${PREFIX}/share/examples/coalesce +DOCFILES= coalesce.doc errors.doc readme +EXFILES= bestree infile intree outfile parmfile seedfile + +do-install: + ${INSTALL_DATA_DIR} ${DOCDIR} + ${INSTALL_DATA_DIR} ${EXDIR} + ${INSTALL_PROGRAM} ${WRKSRC}/coalesce ${PREFIX}/bin/ + for f in ${DOCFILES}; do \ + ${INSTALL_DATA} ${WRKSRC}/$$f ${DOCDIR}/$$f; \ + done + for f in ${EXFILES}; do \ + ${INSTALL_DATA} ${WRKSRC}/$$f ${EXDIR}/$$f; \ + done + +.include "../../mk/bsd.pkg.mk" diff --git a/biology/coalesce/PLIST b/biology/coalesce/PLIST new file mode 100644 index 00000000000..0ff8c903eaa --- /dev/null +++ b/biology/coalesce/PLIST @@ -0,0 +1,13 @@ +@comment $NetBSD: PLIST,v 1.1.1.1 2003/09/30 01:03:56 jschauma Exp $ +bin/coalesce +share/doc/coalesce/coalesce.doc +share/doc/coalesce/errors.doc +share/doc/coalesce/readme +share/examples/coalesce/bestree +share/examples/coalesce/infile +share/examples/coalesce/intree +share/examples/coalesce/outfile +share/examples/coalesce/parmfile +share/examples/coalesce/seedfile +@dirrm share/examples/coalesce +@dirrm share/doc/coalesce diff --git a/biology/coalesce/distinfo b/biology/coalesce/distinfo new file mode 100644 index 00000000000..5119f699c09 --- /dev/null +++ b/biology/coalesce/distinfo @@ -0,0 +1,5 @@ +$NetBSD: distinfo,v 1.1.1.1 2003/09/30 01:03:56 jschauma Exp $ + +SHA1 (coalesce1.5b.tar.gz) = ec2a13da25474440a0c57b2a2e634c94db30961e +Size (coalesce1.5b.tar.gz) = 46153 bytes +SHA1 (patch-aa) = b4c3afcb563c54d4b16f20f8b4b9fc649b49deee diff --git a/biology/coalesce/patches/patch-aa b/biology/coalesce/patches/patch-aa new file mode 100644 index 00000000000..fcc1df0d663 --- /dev/null +++ b/biology/coalesce/patches/patch-aa @@ -0,0 +1,31 @@ +$NetBSD: patch-aa,v 1.1.1.1 2003/09/30 01:03:56 jschauma Exp $ + +--- Makefile.orig 1996-02-29 11:00:09.000000000 -0500 ++++ Makefile 2003-09-29 20:51:32.000000000 -0400 +@@ -1,20 +1,20 @@ + LIBS = -lm + BINDIR = ./bin +-CFLAGS = -g +-CC = cc $(CFLAGS) ++#CFLAGS = -g ++#CC = cc $(CFLAGS) + 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 ++ $(CC) ${CFLAGS} coalesce.c ${LDFLAGS} $(LIBS) -o coalesce + + modellike.o : modellike.c +- $(CC) -c modellike.c ++ $(CC) ${CFLAGS} -c modellike.c + + fluctuate.o : fluctuate.c +- $(CC) -c fluctuate.c ++ $(CC) ${CFLAGS} -c fluctuate.c + + fluctuate : fluctuate.o modellike.o +- $(CC) fluctuate.o modellike.o $(LIBS) -o fluctuate ++ $(CC) ${CFLAGS} fluctuate.o modellike.o ${LDFLAGS} $(LIBS) -o fluctuate |