aboutsummaryrefslogtreecommitdiff
path: root/biology/grappa
diff options
context:
space:
mode:
authorJohann Visagie <wjv@FreeBSD.org>2001-07-04 08:39:40 +0000
committerJohann Visagie <wjv@FreeBSD.org>2001-07-04 08:39:40 +0000
commitf046432f9c655aafb07c6e20150b206fffe830b0 (patch)
tree6351268592432f8944bd2ca7f815a718b613192d /biology/grappa
parent9d8379b1a4d5ff199cf4cae26d25e10e96e0905b (diff)
downloadports-f046432f9c655aafb07c6e20150b206fffe830b0.tar.gz
ports-f046432f9c655aafb07c6e20150b206fffe830b0.zip
Notes
Diffstat (limited to 'biology/grappa')
-rw-r--r--biology/grappa/Makefile25
-rw-r--r--biology/grappa/distinfo1
-rw-r--r--biology/grappa/files/patch-aa16
-rw-r--r--biology/grappa/pkg-comment1
-rw-r--r--biology/grappa/pkg-descr17
-rw-r--r--biology/grappa/pkg-plist3
6 files changed, 63 insertions, 0 deletions
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