From f046432f9c655aafb07c6e20150b206fffe830b0 Mon Sep 17 00:00:00 2001 From: Johann Visagie Date: Wed, 4 Jul 2001 08:39:40 +0000 Subject: Add grappa 1.0.2, Genome Rearrangements Analysis and Phylogeny Software. PR: 28541 Submitted by: dbader@eece.unm.edu --- biology/grappa/Makefile | 25 +++++++++++++++++++++++++ biology/grappa/distinfo | 1 + biology/grappa/files/patch-aa | 16 ++++++++++++++++ biology/grappa/pkg-comment | 1 + biology/grappa/pkg-descr | 17 +++++++++++++++++ biology/grappa/pkg-plist | 3 +++ 6 files changed, 63 insertions(+) create mode 100644 biology/grappa/Makefile create mode 100644 biology/grappa/distinfo create mode 100644 biology/grappa/files/patch-aa create mode 100644 biology/grappa/pkg-comment create mode 100644 biology/grappa/pkg-descr create mode 100644 biology/grappa/pkg-plist (limited to 'biology/grappa') 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 ${PREFIX}/bin/distmat + +.include diff --git a/biology/grappa/distinfo b/biology/grappa/distinfo new file mode 100644 index 000000000000..f1064c764c99 --- /dev/null +++ b/biology/grappa/distinfo @@ -0,0 +1 @@ +MD5 (GRAPPA-1.02.tar.gz) = 198646cf37be9fef0cbaf92dff63fa93 diff --git a/biology/grappa/files/patch-aa b/biology/grappa/files/patch-aa new file mode 100644 index 000000000000..3c9e57471415 --- /dev/null +++ b/biology/grappa/files/patch-aa @@ -0,0 +1,16 @@ +--- Makefile.orig Wed Mar 14 01:21:45 2001 ++++ Makefile Fri Jun 29 20:36:40 2001 +@@ -19,10 +19,10 @@ + + ifeq ($(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 -- cgit v1.2.3