Updated biology/mummer to release 3.18. Changes include:

- MUMmer now resides at Sourceforge
- new tools such as delta-filter
- more extensive html documentation and examples
- bug fixes

5 files changed, 134 insertions, 32 deletions

diff --git a/biology/mummer/Makefile b/biology/mummer/Makefile
index 4f81b15684b..577fa5a32e1 100644
--- a/biology/mummer/Makefile
+++ b/biology/mummer/Makefile
@@ -1,26 +1,26 @@
-# $NetBSD: Makefile,v 1.10 2005/12/05 20:49:51 rillig Exp $
+# $NetBSD: Makefile,v 1.11 2006/01/29 19:31:43 schwarz Exp $
 #
 
-DISTNAME=		MUMmer3.15
-PKGNAME=		mummer-3.15
-PKGREVISION=		1
+DISTNAME=		MUMmer3.18
+PKGNAME=		mummer-3.18
 CATEGORIES=		biology
-MASTER_SITES=		ftp://ftp.tigr.org/pub/software/MUMmer/
+MASTER_SITES=		${MASTER_SITE_SOURCEFORGE:=mummer/}
 
 MAINTAINER=		hdp@cs.nmsu.edu
-HOMEPAGE=		http://www.tigr.org/software/mummer/
+HOMEPAGE=		http://mummer.sourceforge.net/
 COMMENT=		System for aligning whole genome sequences
 
 WRKSRC=			${WRKDIR}/${DISTNAME}
 USE_TOOLS+=		gmake perl:run
+USE_LANGUAGES=		c c++
 
 MAKE_ENV+=		SH=${SH:Q}
 MAKE_ENV+=		PERL=${PERL5:Q}
 INSTALLATION_DIRS=	bin
 
 do-install:
-.for PROGRAM in annotate combineMUMs gaps mgaps mummer repeat-match 	  \
-	show-aligns show-coords show-tiling
+.for PROGRAM in annotate combineMUMs delta-filter gaps mgaps mummer \
+	repeat-match show-aligns show-coords show-snps show-tiling
 	${INSTALL_PROGRAM} ${WRKSRC}/${PROGRAM} ${PREFIX}/bin
 .endfor
 .for PROGRAM in postnuc postpro prenuc prepro
@@ -28,18 +28,46 @@ do-install:
 .endfor
 	${INSTALL_DATA_DIR} ${PREFIX}/share/mummer
 .for SCRIPT in run-mummer1 run-mummer3 nucmer promer exact-tandems 	  \
-	mummerplot nucmer2xfig
+	mapview 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} 		  \
+.for HTML in MUMmer.pdf MUMmer2.pdf MUMmer3.pdf XFiles.pdf \
+	applications.html compare.html index.html logo.gif \
+	mummer-help.gif mummer-users.gif
+	${INSTALL_DATA} ${WRKSRC}/docs/web/${HTML}			\
 		${PREFIX}/share/doc/html/mummer
 .endfor
+	${INSTALL_DATA_DIR} ${PREFIX}/share/doc/html/mummer/examples
+.for HTML in dotplot.gif examples_logo.gif index.html mapplot.gif \
+	mapview_fig.jpg mummer_ps.jpg
+	${INSTALL_DATA} ${WRKSRC}/docs/web/examples/${HTML}		\
+		${PREFIX}/share/doc/html/mummer/examples
+.endfor
+	${INSTALL_DATA_DIR} ${PREFIX}/share/doc/html/mummer/examples/data
+.for DATA in B_anthracis_Mslice.fasta B_anthracis_contigs.fasta \
+	D_melanogaster_2Rslice.cds D_melanogaster_2Rslice.fasta \
+	D_melanogaster_2Rslice.utr D_pseudoobscura_contigs.fasta \
+	H_pylori26695_Bslice.fasta H_pylori26695_Eslice.fasta \
+	H_pyloriJ99_Bslice.fasta H_pyloriJ99_Eslice.fasta README \
+	mapview_0.fig mapview_0.pdf mummer.fplot mummer.gp mummer.mums \
+	mummer.ps mummer.rplot mummer1.align mummer1.errorsgaps \
+	mummer1.gaps mummer1.out mummer3.align mummer3.errorsgaps \
+	mummer3.gaps mummer3.out nucmer.cluster nucmer.coords \
+	nucmer.delta nucmer.snps nucmer.tiling promer.aligns \
+	promer.cluster promer.coords promer.delta
+	${INSTALL_DATA} ${WRKSRC}/docs/web/examples/data/${DATA} 	\
+		${PREFIX}/share/doc/html/mummer/examples/data
+.endfor
+	${INSTALL_DATA_DIR} ${PREFIX}/share/doc/html/mummer/manual
+.for HTML in covplot.gif dotplot.gif gaps.gif index.html 	  \
+	manual_logo.gif mgaps.gif multiplota.gif multiplotb.gif \
+	nuc_proex.gif nucex.gif osi.gif pro_proex.gif
+	${INSTALL_DATA}	${WRKSRC}/docs/web/manual/${HTML} 		  \
+		${PREFIX}/share/doc/html/mummer/manual
+.endfor
 	${INSTALL_DATA_DIR} ${PREFIX}/share/doc/mummer
-.for DOC in maxmat3man.tex maxmat3src.pdf nucmer.README    \
+.for DOC in mapview.README 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
diff --git a/biology/mummer/PLIST b/biology/mummer/PLIST
index 3e853a53bd8..c4c532cbca6 100644
--- a/biology/mummer/PLIST
+++ b/biology/mummer/PLIST
@@ -1,6 +1,7 @@
-@comment $NetBSD: PLIST,v 1.2 2004/12/05 15:24:54 cube Exp $
+@comment $NetBSD: PLIST,v 1.3 2006/01/29 19:31:43 schwarz Exp $
 bin/annotate
 bin/combineMUMs
+bin/delta-filter
 bin/gaps
 bin/mgaps
 bin/mummer
@@ -11,18 +12,72 @@ bin/prepro
 bin/repeat-match
 bin/show-aligns
 bin/show-coords
+bin/show-snps
 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/MUMmer.pdf
+share/doc/html/mummer/MUMmer2.pdf
+share/doc/html/mummer/MUMmer3.pdf
+share/doc/html/mummer/XFiles.pdf
+share/doc/html/mummer/applications.html
+share/doc/html/mummer/compare.html
 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/html/mummer/logo.gif
+share/doc/html/mummer/mummer-help.gif
+share/doc/html/mummer/mummer-users.gif
+share/doc/html/mummer/examples/dotplot.gif
+share/doc/html/mummer/examples/examples_logo.gif
+share/doc/html/mummer/examples/index.html
+share/doc/html/mummer/examples/mapplot.gif
+share/doc/html/mummer/examples/mapview_fig.jpg
+share/doc/html/mummer/examples/mummer_ps.jpg
+share/doc/html/mummer/examples/data/B_anthracis_Mslice.fasta
+share/doc/html/mummer/examples/data/B_anthracis_contigs.fasta
+share/doc/html/mummer/examples/data/D_melanogaster_2Rslice.cds
+share/doc/html/mummer/examples/data/D_melanogaster_2Rslice.fasta
+share/doc/html/mummer/examples/data/D_melanogaster_2Rslice.utr
+share/doc/html/mummer/examples/data/D_pseudoobscura_contigs.fasta
+share/doc/html/mummer/examples/data/H_pylori26695_Bslice.fasta
+share/doc/html/mummer/examples/data/H_pylori26695_Eslice.fasta
+share/doc/html/mummer/examples/data/H_pyloriJ99_Bslice.fasta
+share/doc/html/mummer/examples/data/H_pyloriJ99_Eslice.fasta
+share/doc/html/mummer/examples/data/README
+share/doc/html/mummer/examples/data/mapview_0.fig
+share/doc/html/mummer/examples/data/mapview_0.pdf
+share/doc/html/mummer/examples/data/mummer.fplot
+share/doc/html/mummer/examples/data/mummer.gp
+share/doc/html/mummer/examples/data/mummer.mums
+share/doc/html/mummer/examples/data/mummer.ps
+share/doc/html/mummer/examples/data/mummer.rplot
+share/doc/html/mummer/examples/data/mummer1.align
+share/doc/html/mummer/examples/data/mummer1.errorsgaps
+share/doc/html/mummer/examples/data/mummer1.gaps
+share/doc/html/mummer/examples/data/mummer1.out
+share/doc/html/mummer/examples/data/mummer3.align
+share/doc/html/mummer/examples/data/mummer3.errorsgaps
+share/doc/html/mummer/examples/data/mummer3.gaps
+share/doc/html/mummer/examples/data/mummer3.out
+share/doc/html/mummer/examples/data/nucmer.cluster
+share/doc/html/mummer/examples/data/nucmer.coords
+share/doc/html/mummer/examples/data/nucmer.delta
+share/doc/html/mummer/examples/data/nucmer.snps
+share/doc/html/mummer/examples/data/nucmer.tiling
+share/doc/html/mummer/examples/data/promer.aligns
+share/doc/html/mummer/examples/data/promer.cluster
+share/doc/html/mummer/examples/data/promer.coords
+share/doc/html/mummer/examples/data/promer.delta
+share/doc/html/mummer/manual/covplot.gif
+share/doc/html/mummer/manual/dotplot.gif
+share/doc/html/mummer/manual/gaps.gif
+share/doc/html/mummer/manual/index.html
+share/doc/html/mummer/manual/manual_logo.gif
+share/doc/html/mummer/manual/mgaps.gif
+share/doc/html/mummer/manual/multiplota.gif
+share/doc/html/mummer/manual/multiplotb.gif
+share/doc/html/mummer/manual/nuc_proex.gif
+share/doc/html/mummer/manual/nucex.gif
+share/doc/html/mummer/manual/osi.gif
+share/doc/html/mummer/manual/pro_proex.gif
+share/doc/mummer/mapview.README
 share/doc/mummer/maxmat3man.tex
 share/doc/mummer/maxmat3src.pdf
 share/doc/mummer/nucmer.README
@@ -32,6 +87,7 @@ share/doc/mummer/run-mummer1.README
 share/doc/mummer/run-mummer3.README
 share/doc/mummer/skaff.sty
 share/mummer/exact-tandems
+share/mummer/mapview
 share/mummer/mummerplot
 share/mummer/nucmer
 share/mummer/nucmer2xfig
@@ -41,3 +97,6 @@ share/mummer/run-mummer3
 @dirrm share/mummer
 @dirrm share/doc/mummer
 @dirrm share/doc/html/mummer
+@dirrm share/doc/html/mummer/manual
+@dirrm share/doc/html/mummer/examples
+@dirrm share/doc/html/mummer/examples/data
diff --git a/biology/mummer/distinfo b/biology/mummer/distinfo
index ff411468bd5..65e4d6f199b 100644
--- a/biology/mummer/distinfo
+++ b/biology/mummer/distinfo
@@ -1,7 +1,8 @@
-$NetBSD: distinfo,v 1.4 2005/06/19 01:13:23 kristerw Exp $
+$NetBSD: distinfo,v 1.5 2006/01/29 19:31:43 schwarz Exp $
 
-SHA1 (MUMmer3.15.tar.gz) = c8907b0b2010e3a8d07fff0dde570c12d9cf8dea
-RMD160 (MUMmer3.15.tar.gz) = 223135f09c8795f7fab5219f07c7047f114056df
-Size (MUMmer3.15.tar.gz) = 660102 bytes
-SHA1 (patch-aa) = bf64019cbbfa53c1883641b28186146cd7c0a946
+SHA1 (MUMmer3.18.tar.gz) = 484846f7ff68e19bc0e0deca92254fd423947a9f
+RMD160 (MUMmer3.18.tar.gz) = 7361a90d28e2432a9163e0745ab854dfd31cf306
+Size (MUMmer3.18.tar.gz) = 3069437 bytes
+SHA1 (patch-aa) = 369c4646b01acb4607aae933b70a08448331c3e6
 SHA1 (patch-ab) = 8548bc11a6d43b489ea9af5dbca584ce0d2750c9
+SHA1 (patch-ac) = 7f0f16bdd83bc80833f1ffdcfe1bad7c2ee76eec
diff --git a/biology/mummer/patches/patch-aa b/biology/mummer/patches/patch-aa
index 594e90a0e33..6fed9c79204 100644
--- a/biology/mummer/patches/patch-aa
+++ b/biology/mummer/patches/patch-aa
@@ -1,4 +1,4 @@
-$NetBSD: patch-aa,v 1.2 2004/12/05 15:24:54 cube Exp $
+$NetBSD: patch-aa,v 1.3 2006/01/29 19:31:43 schwarz Exp $
 
 --- Makefile.orig	2003-07-09 09:49:51.000000000 -0400
 +++ Makefile	2003-09-27 18:15:34.000000000 -0400
@@ -8,7 +8,7 @@ $NetBSD: patch-aa,v 1.2 2004/12/05 15:24:54 cube Exp $
  #-------------------------------------------------------------------------------
 -SHELL = /bin/sh
 +SHELL = ${SH}
- VERSION := 3.15
+ VERSION := 3.18
  
  
 @@ -35,15 +35,12 @@
diff --git a/biology/mummer/patches/patch-ac b/biology/mummer/patches/patch-ac
new file mode 100644
index 00000000000..c53022e5c9a
--- /dev/null
+++ b/biology/mummer/patches/patch-ac
@@ -0,0 +1,14 @@
+$NetBSD: patch-ac,v 1.1 2006/01/29 19:31:43 schwarz Exp $
+
+--- src/kurtz/libbasedir/mapfile.c.orig	2006-01-28 12:08:35.000000000 +0100
++++ src/kurtz/libbasedir/mapfile.c	2006-01-28 12:09:24.000000000 +0100
+@@ -157,6 +157,9 @@
+                     MAP_PRIVATE,
+                     fd,
+                     (off_t) 0);
++#ifndef MAP_FAILED
++#define MAP_FAILED	((void *) -1)
++#endif
+   if(memoryptr[fd] == (void *) MAP_FAILED)
+   {
+     ERROR1("memorymapping for filedescriptor %ld failed",(Showsint) fd);