From 4e03a01d5ae09c7b3936d175311853a56f5ab4ea Mon Sep 17 00:00:00 2001 From: jschauma Date: Tue, 30 Sep 2003 01:19:31 +0000 Subject: Initial import of fluctuate, one of the many packages provided by brook at biology dot nmsu dot edu and his team at NMSU. 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. --- biology/fluctuate/DESCR | 5 +++++ biology/fluctuate/MESSAGE | 9 ++++++++ biology/fluctuate/Makefile | 33 ++++++++++++++++++++++++++++ biology/fluctuate/PLIST | 9 ++++++++ biology/fluctuate/distinfo | 5 +++++ biology/fluctuate/patches/patch-aa | 45 ++++++++++++++++++++++++++++++++++++++ 6 files changed, 106 insertions(+) create mode 100644 biology/fluctuate/DESCR create mode 100644 biology/fluctuate/MESSAGE create mode 100644 biology/fluctuate/Makefile create mode 100644 biology/fluctuate/PLIST create mode 100644 biology/fluctuate/distinfo create mode 100644 biology/fluctuate/patches/patch-aa (limited to 'biology') diff --git a/biology/fluctuate/DESCR b/biology/fluctuate/DESCR new file mode 100644 index 00000000000..ca4211c0edc --- /dev/null +++ b/biology/fluctuate/DESCR @@ -0,0 +1,5 @@ +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. diff --git a/biology/fluctuate/MESSAGE b/biology/fluctuate/MESSAGE new file mode 100644 index 00000000000..9df14f254b0 --- /dev/null +++ b/biology/fluctuate/MESSAGE @@ -0,0 +1,9 @@ +=========================================================================== +$NetBSD: MESSAGE,v 1.1.1.1 2003/09/30 01:19:31 jschauma Exp $ + +In order to run the fluctuate example, you should create a directory for +example files and then copy ${PREFIX}/share/examples/fluctuate/{bestree, +infile,outfile} to there. After that, you can simply run 'fluctuate' from +that directory. + +=========================================================================== diff --git a/biology/fluctuate/Makefile b/biology/fluctuate/Makefile new file mode 100644 index 00000000000..99c8a1cd405 --- /dev/null +++ b/biology/fluctuate/Makefile @@ -0,0 +1,33 @@ +# $NetBSD: Makefile,v 1.1.1.1 2003/09/30 01:19:31 jschauma Exp $ +# + +DISTNAME= fluctuate1.4.src.doc +PKGNAME= fluctuate-1.4 +WRKSRC= ${WRKDIR}/fluctuate1.4 +CATEGORIES= biology +MASTER_SITES= ftp://evolution.genetics.washington.edu/pub/lamarc/fluctuate/ + +MAINTAINER= brook@nmsu.edu +HOMEPAGE= http://evolution.genetics.washington.edu/lamarc/fluctuate.html +COMMENT= Estimation of population growth rate + +USE_BUILDLINK2= YES +ALL_TARGET= fluctuate + +DOCDIR= ${PREFIX}/share/doc/fluctuate +EXDIR= ${PREFIX}/share/examples/fluctuate +DOCFILES= fluctuate.doc errors.doc +EXFILES= bestree infile outfile + +do-install: + ${INSTALL_PROGRAM} ${WRKSRC}/fluctuate ${PREFIX}/bin/ + ${INSTALL_DATA_DIR} ${DOCDIR} + ${INSTALL_DATA_DIR} ${EXDIR} + 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/fluctuate/PLIST b/biology/fluctuate/PLIST new file mode 100644 index 00000000000..66ae75d4508 --- /dev/null +++ b/biology/fluctuate/PLIST @@ -0,0 +1,9 @@ +@comment $NetBSD: PLIST,v 1.1.1.1 2003/09/30 01:19:31 jschauma Exp $ +bin/fluctuate +share/doc/fluctuate/errors.doc +share/doc/fluctuate/fluctuate.doc +share/examples/fluctuate/bestree +share/examples/fluctuate/infile +share/examples/fluctuate/outfile +@dirrm share/examples/fluctuate +@dirrm share/doc/fluctuate diff --git a/biology/fluctuate/distinfo b/biology/fluctuate/distinfo new file mode 100644 index 00000000000..eb05ed6d21b --- /dev/null +++ b/biology/fluctuate/distinfo @@ -0,0 +1,5 @@ +$NetBSD: distinfo,v 1.1.1.1 2003/09/30 01:19:31 jschauma Exp $ + +SHA1 (fluctuate1.4.src.doc.tar.gz) = 7e9fb766312237f85a191327aae37c9a52a2e408 +Size (fluctuate1.4.src.doc.tar.gz) = 70690 bytes +SHA1 (patch-aa) = d7637d2d2b47d9ceb920319393f13e84a60bfae0 diff --git a/biology/fluctuate/patches/patch-aa b/biology/fluctuate/patches/patch-aa new file mode 100644 index 00000000000..65ad09b6be9 --- /dev/null +++ b/biology/fluctuate/patches/patch-aa @@ -0,0 +1,45 @@ +$NetBSD: patch-aa,v 1.1.1.1 2003/09/30 01:19:32 jschauma Exp $ + +--- Makefile.orig 2003-09-29 21:08:30.000000000 -0400 ++++ Makefile 2003-09-29 21:09:31.000000000 -0400 +@@ -1,30 +1,30 @@ + LIBS = -lm + BINDIR = ./bin +-CFLAGS = -O2 -funroll-loops +-CC = gcc $(CFLAGS) ++CFLAGS += -O2 -funroll-loops ++#CC = gcc $(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 \ +- coal_modellike.o $(LIBS) -o fluctuate ++ $(CC) ${CFLAGS} fluctuate.o fluc_modellike.o getdata.o plot.o wrap.o \ ++ coal_modellike.o ${LDFLAGS} $(LIBS) -o fluctuate + + clean : + rm fluctuate.o fluc_modellike.o coal_modellike.o getdata.o plot.o wrap.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 -- cgit v1.2.3