[pkgsrc/trunk]: pkgsrc/biology/coalesce Initial import of coalesce, one of th...

[jschauma <jschauma%pkgsrc.org@localhost>]

details:   https://anonhg.NetBSD.org/pkgsrc/rev/d1c9b215f1d5
branches:  trunk
changeset: 462289:d1c9b215f1d5
user:      jschauma <jschauma%pkgsrc.org@localhost>
date:      Tue Sep 30 01:03:56 2003 +0000

description:
Initial import of coalesce, one of the many packages provided by
brook at biology dot nmsu dot edu and his team at NMSU.

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.

diffstat:

 biology/coalesce/DESCR            |   3 +++
 biology/coalesce/Makefile         |  33 +++++++++++++++++++++++++++++++++
 biology/coalesce/PLIST            |  13 +++++++++++++
 biology/coalesce/distinfo         |   5 +++++
 biology/coalesce/patches/patch-aa |  31 +++++++++++++++++++++++++++++++
 5 files changed, 85 insertions(+), 0 deletions(-)

diffs (105 lines):

diff -r df5796a61c7a -r d1c9b215f1d5 biology/coalesce/DESCR
--- /dev/null   Thu Jan 01 00:00:00 1970 +0000
+++ b/biology/coalesce/DESCR    Tue Sep 30 01:03:56 2003 +0000
@@ -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 -r df5796a61c7a -r d1c9b215f1d5 biology/coalesce/Makefile
--- /dev/null   Thu Jan 01 00:00:00 1970 +0000
+++ b/biology/coalesce/Makefile Tue Sep 30 01:03:56 2003 +0000
@@ -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@localhost
+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 -r df5796a61c7a -r d1c9b215f1d5 biology/coalesce/PLIST
--- /dev/null   Thu Jan 01 00:00:00 1970 +0000
+++ b/biology/coalesce/PLIST    Tue Sep 30 01:03:56 2003 +0000
@@ -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 -r df5796a61c7a -r d1c9b215f1d5 biology/coalesce/distinfo
--- /dev/null   Thu Jan 01 00:00:00 1970 +0000
+++ b/biology/coalesce/distinfo Tue Sep 30 01:03:56 2003 +0000
@@ -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 -r df5796a61c7a -r d1c9b215f1d5 biology/coalesce/patches/patch-aa
--- /dev/null   Thu Jan 01 00:00:00 1970 +0000
+++ b/biology/coalesce/patches/patch-aa Tue Sep 30 01:03:56 2003 +0000
@@ -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