Add grappa 1.0.2, Genome Rearrangements Analysis and Phylogeny

Software.

PR:		28541
Submitted by:	dbader@eece.unm.edu

7 files changed, 64 insertions, 0 deletions

diff --git a/biology/Makefile b/biology/Makefile
index db5520e84928..5632f6133881 100644
--- a/biology/Makefile
+++ b/biology/Makefile
@@ -13,6 +13,7 @@
     SUBDIR += gaussian98
     SUBDIR += genpak
     SUBDIR += gperiodic
+    SUBDIR += grappa
     SUBDIR += hmmer
     SUBDIR += kinemage
     SUBDIR += molden
diff --git a/biology/grappa/Makefile b/biology/grappa/Makefile
new file mode 100644
index 000000000000..7324eef521eb
--- /dev/null
+++ b/biology/grappa/Makefile
@@ -0,0 +1,25 @@
+# New ports collection makefile for:	grappa
+# Date created:		30 June 2001
+# Whom:                 dbader@eece.unm.edu
+#
+# $FreeBSD$
+#
+
+PORTNAME=	grappa
+PORTVERSION=	1.0.2
+CATEGORIES=	biology
+MASTER_SITES=	http://www.cs.unm.edu/~moret/
+DISTNAME=	GRAPPA-1.02
+
+MAINTAINER=	dbader@eece.unm.edu
+
+BUILD_DEPENDS=	${LOCALBASE}/lib/libconcorde.a:${PORTSDIR}/math/concorde
+
+USE_GMAKE=	yes
+
+do-install:
+	${INSTALL_PROGRAM} ${WRKSRC}/grappa ${PREFIX}/bin
+	${LN} -sf ${PREFIX}/bin/grappa ${PREFIX}/bin/invdist
+	${LN} -sf ${PREFIX}/bin/grappa ${PREFIX}/bin/distmat
+
+.include <bsd.port.mk>
diff --git a/biology/grappa/distinfo b/biology/grappa/distinfo
new file mode 100644
index 000000000000..f1064c764c99
--- /dev/null
+++ b/biology/grappa/distinfo
@@ -0,0 +1 @@
+MD5 (GRAPPA-1.02.tar.gz) = 198646cf37be9fef0cbaf92dff63fa93
diff --git a/biology/grappa/files/patch-aa b/biology/grappa/files/patch-aa
new file mode 100644
index 000000000000..3c9e57471415
--- /dev/null
+++ b/biology/grappa/files/patch-aa
@@ -0,0 +1,16 @@
+--- Makefile.orig	Wed Mar 14 01:21:45 2001
++++ Makefile	Fri Jun 29 20:36:40 2001
+@@ -19,10 +19,10 @@
+ 
+ ifeq ($(USE_CONCORDE),YES)
+ # Set CONCORDE_ROOT to the location of the compiler concorde libraries
+-  CONCORDE_ROOT   = $(HOME)/concorde
+-  CONCORDE_INC    = $(CONCORDE_ROOT)/INCLUDE
++  CONCORDE_ROOT   = /usr/local
++  CONCORDE_INC    = $(CONCORDE_ROOT)/include/concorde
+   CONCORDE_CFLAGS = -I$(CONCORDE_INC) -DCONCORDE
+-  CONCORDE_LIB    = $(CONCORDE_ROOT)/concorde.a
++  CONCORDE_LIB    = $(CONCORDE_ROOT)/lib/libconcorde.a
+ else
+   CONCORDE_CFLAGS =
+   CONCORDE_LIB    =
diff --git a/biology/grappa/pkg-comment b/biology/grappa/pkg-comment
new file mode 100644
index 000000000000..42cf72c3f8ed
--- /dev/null
+++ b/biology/grappa/pkg-comment
@@ -0,0 +1 @@
+Genome Rearrangements Analysis and Phylogeny Software
diff --git a/biology/grappa/pkg-descr b/biology/grappa/pkg-descr
new file mode 100644
index 000000000000..ce732438a251
--- /dev/null
+++ b/biology/grappa/pkg-descr
@@ -0,0 +1,17 @@
+GRAPPA: Genome Rearrangements Analysis under Parsimony and other
+Phylogenetic Algorithms
+				     
+This suite of programs implements the approach to phylogeny
+reconstruction from gene orders described in the paper
+   Moret, B.M.E., Wyman, S., Bader, D.A., Warnow, T., and Yan, M.,
+   ``A detailed study of breakpoint analysis,''
+   Proc. 6th Pacific Symp. Biocomputing PSB 2001, Hawaii (2001).
+In its current state, "grappa" allows one to explore either the
+space of all possible trees on n labelled leaves or the space of all
+such trees that obey (are refinements of) a particular constraint tree.
+
+"invdist" takes the first two genomes in the input file and returns
+their inversion distance.
+"distmat" prints the inversion and breakpoint distance matrices. 
+
+WWW: http://www.cs.unm.edu/~moret/GRAPPA/
diff --git a/biology/grappa/pkg-plist b/biology/grappa/pkg-plist
new file mode 100644
index 000000000000..3e22e0450c58
--- /dev/null
+++ b/biology/grappa/pkg-plist
@@ -0,0 +1,3 @@
+bin/grappa
+bin/invdist
+bin/distmat