Initial import of mummer, one of the many packages provided by

brook at biology dot nmsu dot edu and his team at NMSU.

Mummer is a system for aligning whole genome sequences. Using an efficient
data structure called a suffix tree, the system is able rapidly to align
sequences containing millions of nucleotides whether in complete or draft
form. MUMmer can also align incomplete genomes; it handles the 100s or 1000s
of contigs from a shotgun sequencing project with ease, and will align them to
another set of contigs or a genome using the NUCmer program included with the
system. 

5 files changed, 137 insertions, 0 deletions

diff --git a/biology/mummer/DESCR b/biology/mummer/DESCR
new file mode 100644
index 00000000000..d265928f73e
--- /dev/null
+++ b/biology/mummer/DESCR
@@ -0,0 +1,7 @@
+Mummer is a system for aligning whole genome sequences. Using an efficient
+data structure called a suffix tree, the system is able rapidly to align
+sequences containing millions of nucleotides whether in complete or draft
+form. MUMmer can also align incomplete genomes; it handles the 100s or 1000s
+of contigs from a shotgun sequencing project with ease, and will align them to
+another set of contigs or a genome using the NUCmer program included with the
+system. 
diff --git a/biology/mummer/Makefile b/biology/mummer/Makefile
new file mode 100644
index 00000000000..af83ff789c7
--- /dev/null
+++ b/biology/mummer/Makefile
@@ -0,0 +1,47 @@
+# $NetBSD: Makefile,v 1.1.1.1 2003/09/27 22:24:56 jschauma Exp $
+#
+
+DISTNAME=		MUMmer3.04
+PKGNAME=		mummer-3.04
+WRKSRC=			${WRKDIR}/${DISTNAME}
+CATEGORIES=		biology
+MASTER_SITES=		ftp://ftp.tigr.org/pub/software/MUMmer/
+
+MAINTAINER=		hdp@cs.nmsu.edu
+HOMEPAGE=		http://www.tigr.org/software/mummer/
+COMMENT=		System for aligning whole genome sequences
+
+USE_BUILDLINK2=		YES
+USE_GNU_TOOLS+=		make
+
+MAKE_ENV+=		SH="${SH}"
+
+do-install:
+.for PROGRAM in annotate combineMUMs gaps mgaps mummer repeat-match 	  \
+	show-aligns show-coords show-tiling
+	${INSTALL_PROGRAM} ${WRKSRC}/${PROGRAM} ${PREFIX}/bin
+.endfor
+.for PROGRAM in postnuc postpro prenuc prepro
+	${INSTALL_PROGRAM} ${WRKSRC}/aux_bin/${PROGRAM} ${PREFIX}/bin
+.endfor
+	${INSTALL_DATA_DIR} ${PREFIX}/share/mummer
+.for SCRIPT in run-mummer1 run-mummer3 nucmer promer exact-tandems 	  \
+	mummerplot nucmer2xfig
+	${INSTALL_SCRIPT} ${WRKSRC}/${SCRIPT} ${PREFIX}/share/mummer
+.endfor
+	${INSTALL_DATA_DIR} ${PREFIX}/share/doc/html/mummer
+.for HTML in covplot.gif dotplot.gif email.jpg gaps.gif index.html 	  \
+	manual_logo.gif mgaps.gif nuc_proex.gif nucex.gif osi.gif 	  \
+	pro_proex.gif
+	${INSTALL_DATA}	${WRKSRC}/docs/htmlmanual/${HTML} 		  \
+		${PREFIX}/share/doc/html/mummer
+.endfor
+	${INSTALL_DATA_DIR} ${PREFIX}/share/doc/mummer
+.for DOC in maxmat3man.pdf maxmat3man.tex maxmat3src.pdf nucmer.README    \
+	optionman.sty promer.README run-mummer1.README run-mummer3.README \
+	skaff.sty
+	${INSTALL_DATA} ${WRKSRC}/docs/${DOC} ${PREFIX}/share/doc/mummer
+.endfor
+
+.include "../../lang/perl5/buildlink2.mk"
+.include "../../mk/bsd.pkg.mk"
diff --git a/biology/mummer/PLIST b/biology/mummer/PLIST
new file mode 100644
index 00000000000..ae9522e6679
--- /dev/null
+++ b/biology/mummer/PLIST
@@ -0,0 +1,44 @@
+@comment $NetBSD: PLIST,v 1.1.1.1 2003/09/27 22:24:57 jschauma Exp $
+bin/annotate
+bin/combineMUMs
+bin/gaps
+bin/mgaps
+bin/mummer
+bin/postnuc
+bin/postpro
+bin/prenuc
+bin/prepro
+bin/repeat-match
+bin/show-aligns
+bin/show-coords
+bin/show-tiling
+share/doc/html/mummer/covplot.gif
+share/doc/html/mummer/dotplot.gif
+share/doc/html/mummer/email.jpg
+share/doc/html/mummer/gaps.gif
+share/doc/html/mummer/index.html
+share/doc/html/mummer/manual_logo.gif
+share/doc/html/mummer/mgaps.gif
+share/doc/html/mummer/nuc_proex.gif
+share/doc/html/mummer/nucex.gif
+share/doc/html/mummer/osi.gif
+share/doc/html/mummer/pro_proex.gif
+share/doc/mummer/maxmat3man.pdf
+share/doc/mummer/maxmat3man.tex
+share/doc/mummer/maxmat3src.pdf
+share/doc/mummer/nucmer.README
+share/doc/mummer/optionman.sty
+share/doc/mummer/promer.README
+share/doc/mummer/run-mummer1.README
+share/doc/mummer/run-mummer3.README
+share/doc/mummer/skaff.sty
+share/mummer/exact-tandems
+share/mummer/mummerplot
+share/mummer/nucmer
+share/mummer/nucmer2xfig
+share/mummer/promer
+share/mummer/run-mummer1
+share/mummer/run-mummer3
+@dirrm share/mummer
+@dirrm share/doc/mummer
+@dirrm share/doc/html/mummer
diff --git a/biology/mummer/distinfo b/biology/mummer/distinfo
new file mode 100644
index 00000000000..5d4bcb3d4d9
--- /dev/null
+++ b/biology/mummer/distinfo
@@ -0,0 +1,5 @@
+$NetBSD: distinfo,v 1.1.1.1 2003/09/27 22:24:57 jschauma Exp $
+
+SHA1 (MUMmer3.04.tar.gz) = e0f17d535a857bd9b3059d5d0a951621f89041b2
+Size (MUMmer3.04.tar.gz) = 835629 bytes
+SHA1 (patch-aa) = 39253c79e7239365dfdcee46c410f234a23c6df0
diff --git a/biology/mummer/patches/patch-aa b/biology/mummer/patches/patch-aa
new file mode 100644
index 00000000000..e941dc25546
--- /dev/null
+++ b/biology/mummer/patches/patch-aa
@@ -0,0 +1,34 @@
+$NetBSD: patch-aa,v 1.1.1.1 2003/09/27 22:24:57 jschauma Exp $
+
+--- Makefile.orig	2003-07-09 09:49:51.000000000 -0400
++++ Makefile	2003-09-27 18:15:34.000000000 -0400
+@@ -22,7 +22,7 @@
+ #  'make uninstall' alias for 'make clean' (for compatibility)
+ #
+ #-------------------------------------------------------------------------------
+-SHELL = /bin/sh
++SHELL = ${SH}
+ VERSION := 3.04
+ 
+ 
+@@ -35,15 +35,12 @@
+ TIGR_SRC_DIR  := $(TOP_DIR)/src/tigr
+ KURTZ_SRC_DIR := $(TOP_DIR)/src/kurtz
+ 
+-CC   := $(filter /%,$(shell /bin/sh -c 'type gcc'))
+-CXX  := $(filter /%,$(shell /bin/sh -c 'type g++'))
+-SED  := $(filter /%,$(shell /bin/sh -c 'type sed'))
++#CC   := $(filter /%,$(shell /bin/sh -c 'type gcc'))
++#CXX  := $(filter /%,$(shell /bin/sh -c 'type g++'))
++#SED  := $(filter /%,$(shell /bin/sh -c 'type sed'))
+ CSH  := $(filter /%,$(shell /bin/sh -c 'type csh'))
+-PERL := $(filter /%,$(shell /bin/sh -c 'type perl'))
+-AR   := $(filter /%,$(shell /bin/sh -c 'type ar'))
+-
+-CPPFLAGS = -Wall -O3
+-LDFLAGS  =
++#PERL := $(filter /%,$(shell /bin/sh -c 'type perl'))
++#AR   := $(filter /%,$(shell /bin/sh -c 'type ar'))
+ 
+ FLATS = ACKNOWLEDGEMENTS COPYRIGHT INSTALL LICENSE Makefile README
+