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[pkgsrc/trunk]: pkgsrc/biology/fluctuate Initial import of fluctuate, one of ...
details: https://anonhg.NetBSD.org/pkgsrc/rev/fe9ff282d746
branches: trunk
changeset: 462292:fe9ff282d746
user: jschauma <jschauma%pkgsrc.org@localhost>
date: Tue Sep 30 01:19:31 2003 +0000
description:
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.
diffstat:
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(+), 0 deletions(-)
diffs (130 lines):
diff -r 83ed75d80b33 -r fe9ff282d746 biology/fluctuate/DESCR
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/biology/fluctuate/DESCR Tue Sep 30 01:19:31 2003 +0000
@@ -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 -r 83ed75d80b33 -r fe9ff282d746 biology/fluctuate/MESSAGE
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/biology/fluctuate/MESSAGE Tue Sep 30 01:19:31 2003 +0000
@@ -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 -r 83ed75d80b33 -r fe9ff282d746 biology/fluctuate/Makefile
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/biology/fluctuate/Makefile Tue Sep 30 01:19:31 2003 +0000
@@ -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@localhost
+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 -r 83ed75d80b33 -r fe9ff282d746 biology/fluctuate/PLIST
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/biology/fluctuate/PLIST Tue Sep 30 01:19:31 2003 +0000
@@ -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 -r 83ed75d80b33 -r fe9ff282d746 biology/fluctuate/distinfo
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/biology/fluctuate/distinfo Tue Sep 30 01:19:31 2003 +0000
@@ -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 -r 83ed75d80b33 -r fe9ff282d746 biology/fluctuate/patches/patch-aa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/biology/fluctuate/patches/patch-aa Tue Sep 30 01:19:31 2003 +0000
@@ -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
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