Updated mummer to 3.19.

Changes since 3.18:
- More documentation.

4 files changed, 91 insertions, 128 deletions

diff --git a/biology/mummer/Makefile b/biology/mummer/Makefile
index fb7a8d110a2..97281c2c9c3 100644
--- a/biology/mummer/Makefile
+++ b/biology/mummer/Makefile
@@ -1,9 +1,8 @@
-# $NetBSD: Makefile,v 1.14 2006/12/06 16:52:20 joerg Exp $
+# $NetBSD: Makefile,v 1.15 2007/01/18 19:13:10 rillig Exp $
 #
 
-DISTNAME=		MUMmer3.18
-PKGNAME=		mummer-3.18
-PKGREVISION=		3
+DISTNAME=		MUMmer3.19
+PKGNAME=		mummer-3.19
 CATEGORIES=		biology
 MASTER_SITES=		${MASTER_SITE_SOURCEFORGE:=mummer/}
 
@@ -18,61 +17,20 @@ USE_LANGUAGES=		c c++
 MAKE_ENV+=		SH=${SH:Q}
 MAKE_ENV+=		PERL=${PERL5:Q}
 MAKE_ENV+=		CSH=${TOOLS_PATH.csh:Q}
-INSTALLATION_DIRS=	bin
+INSTALLATION_DIRS=	bin share/doc/mummer share/mummer
 
 do-install:
-.for PROGRAM in annotate combineMUMs delta-filter gaps mgaps mummer \
+.for p in annotate combineMUMs delta-filter gaps mgaps mummer \
 	repeat-match show-aligns show-coords show-snps show-tiling
-	${INSTALL_PROGRAM} ${WRKSRC}/${PROGRAM} ${PREFIX}/bin
+	${INSTALL_PROGRAM} ${WRKSRC}/${p} ${PREFIX}/bin
 .endfor
-.for PROGRAM in postnuc postpro prenuc prepro
-	${INSTALL_PROGRAM} ${WRKSRC}/aux_bin/${PROGRAM} ${PREFIX}/bin
+.for p in postnuc postpro prenuc prepro
+	${INSTALL_PROGRAM} ${WRKSRC}/aux_bin/${p} ${PREFIX}/bin
 .endfor
-	${INSTALL_DATA_DIR} ${PREFIX}/share/mummer
-.for SCRIPT in run-mummer1 run-mummer3 nucmer promer exact-tandems 	  \
+.for f in run-mummer1 run-mummer3 nucmer promer exact-tandems 	  \
 	mapview mummerplot nucmer2xfig
-	${INSTALL_SCRIPT} ${WRKSRC}/${SCRIPT} ${PREFIX}/share/mummer
-.endfor
-	${INSTALL_DATA_DIR} ${PREFIX}/share/doc/html/mummer
-.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 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
+	${INSTALL_SCRIPT} ${WRKSRC}/${f} ${PREFIX}/share/mummer
 .endfor
+	cd ${WRKSRC}/docs && pax -wr -s ',^Makefile$$,,' * ${PREFIX}/share/doc/mummer
 
 .include "../../mk/bsd.pkg.mk"
diff --git a/biology/mummer/PLIST b/biology/mummer/PLIST
index aa8ba4fdc12..32948e95ba5 100644
--- a/biology/mummer/PLIST
+++ b/biology/mummer/PLIST
@@ -1,4 +1,4 @@
-@comment $NetBSD: PLIST,v 1.4 2006/06/21 19:01:12 minskim Exp $
+@comment $NetBSD: PLIST,v 1.5 2007/01/18 19:13:10 rillig Exp $
 bin/annotate
 bin/combineMUMs
 bin/delta-filter
@@ -14,69 +14,8 @@ bin/show-aligns
 bin/show-coords
 bin/show-snps
 bin/show-tiling
-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/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/README
+share/doc/mummer/differences.README
 share/doc/mummer/mapview.README
 share/doc/mummer/maxmat3man.tex
 share/doc/mummer/maxmat3src.pdf
@@ -86,6 +25,72 @@ share/doc/mummer/promer.README
 share/doc/mummer/run-mummer1.README
 share/doc/mummer/run-mummer3.README
 share/doc/mummer/skaff.sty
+share/doc/mummer/web/MUMmer.pdf
+share/doc/mummer/web/MUMmer2.pdf
+share/doc/mummer/web/MUMmer3.pdf
+share/doc/mummer/web/XFiles.pdf
+share/doc/mummer/web/applications.html
+share/doc/mummer/web/compare.html
+share/doc/mummer/web/examples/data/B_anthracis_Mslice.fasta
+share/doc/mummer/web/examples/data/B_anthracis_contigs.fasta
+share/doc/mummer/web/examples/data/D_melanogaster_2Rslice.cds
+share/doc/mummer/web/examples/data/D_melanogaster_2Rslice.fasta
+share/doc/mummer/web/examples/data/D_melanogaster_2Rslice.utr
+share/doc/mummer/web/examples/data/D_pseudoobscura_contigs.fasta
+share/doc/mummer/web/examples/data/H_pylori26695_Bslice.fasta
+share/doc/mummer/web/examples/data/H_pylori26695_Eslice.fasta
+share/doc/mummer/web/examples/data/H_pyloriJ99_Bslice.fasta
+share/doc/mummer/web/examples/data/H_pyloriJ99_Eslice.fasta
+share/doc/mummer/web/examples/data/README
+share/doc/mummer/web/examples/data/mapview_0.fig
+share/doc/mummer/web/examples/data/mapview_0.pdf
+share/doc/mummer/web/examples/data/mummer.fplot
+share/doc/mummer/web/examples/data/mummer.gp
+share/doc/mummer/web/examples/data/mummer.mums
+share/doc/mummer/web/examples/data/mummer.ps
+share/doc/mummer/web/examples/data/mummer.rplot
+share/doc/mummer/web/examples/data/mummer1.align
+share/doc/mummer/web/examples/data/mummer1.errorsgaps
+share/doc/mummer/web/examples/data/mummer1.gaps
+share/doc/mummer/web/examples/data/mummer1.out
+share/doc/mummer/web/examples/data/mummer3.align
+share/doc/mummer/web/examples/data/mummer3.errorsgaps
+share/doc/mummer/web/examples/data/mummer3.gaps
+share/doc/mummer/web/examples/data/mummer3.out
+share/doc/mummer/web/examples/data/nucmer.cluster
+share/doc/mummer/web/examples/data/nucmer.coords
+share/doc/mummer/web/examples/data/nucmer.delta
+share/doc/mummer/web/examples/data/nucmer.snps
+share/doc/mummer/web/examples/data/nucmer.tiling
+share/doc/mummer/web/examples/data/promer.aligns
+share/doc/mummer/web/examples/data/promer.cluster
+share/doc/mummer/web/examples/data/promer.coords
+share/doc/mummer/web/examples/data/promer.delta
+share/doc/mummer/web/examples/dotplot.gif
+share/doc/mummer/web/examples/examples_logo.gif
+share/doc/mummer/web/examples/index.html
+share/doc/mummer/web/examples/mapplot.gif
+share/doc/mummer/web/examples/mapview_fig.jpg
+share/doc/mummer/web/examples/mummer_ps.jpg
+share/doc/mummer/web/index.html
+share/doc/mummer/web/logo.gif
+share/doc/mummer/web/manual/AlignmentTypes.odg
+share/doc/mummer/web/manual/AlignmentTypes.pdf
+share/doc/mummer/web/manual/covplot.gif
+share/doc/mummer/web/manual/dotplot.gif
+share/doc/mummer/web/manual/gaps.gif
+share/doc/mummer/web/manual/index.html
+share/doc/mummer/web/manual/manual_logo.gif
+share/doc/mummer/web/manual/mapplot.gif
+share/doc/mummer/web/manual/mgaps.gif
+share/doc/mummer/web/manual/multiplota.gif
+share/doc/mummer/web/manual/multiplotb.gif
+share/doc/mummer/web/manual/nuc_proex.gif
+share/doc/mummer/web/manual/nucex.gif
+share/doc/mummer/web/manual/osi.gif
+share/doc/mummer/web/manual/pro_proex.gif
+share/doc/mummer/web/mummer-help.gif
+share/doc/mummer/web/mummer-users.gif
 share/mummer/exact-tandems
 share/mummer/mapview
 share/mummer/mummerplot
@@ -95,8 +100,8 @@ share/mummer/promer
 share/mummer/run-mummer1
 share/mummer/run-mummer3
 @dirrm share/mummer
+@dirrm share/doc/mummer/web/manual
+@dirrm share/doc/mummer/web/examples/data
+@dirrm share/doc/mummer/web/examples
+@dirrm share/doc/mummer/web
 @dirrm share/doc/mummer
-@dirrm share/doc/html/mummer/examples/data
-@dirrm share/doc/html/mummer/examples
-@dirrm share/doc/html/mummer/manual
-@dirrm share/doc/html/mummer
diff --git a/biology/mummer/distinfo b/biology/mummer/distinfo
index b7e98faead1..45af2ccb057 100644
--- a/biology/mummer/distinfo
+++ b/biology/mummer/distinfo
@@ -1,9 +1,9 @@
-$NetBSD: distinfo,v 1.7 2006/12/06 16:52:20 joerg Exp $
+$NetBSD: distinfo,v 1.8 2007/01/18 19:13:10 rillig Exp $
 
-SHA1 (MUMmer3.18.tar.gz) = 484846f7ff68e19bc0e0deca92254fd423947a9f
-RMD160 (MUMmer3.18.tar.gz) = 7361a90d28e2432a9163e0745ab854dfd31cf306
-Size (MUMmer3.18.tar.gz) = 3069437 bytes
-SHA1 (patch-aa) = 707f0466ac20b58feb22a5fd525f5f8d9df31dac
+SHA1 (MUMmer3.19.tar.gz) = 8906bab6bd43b307461de8b5f44122a115799533
+RMD160 (MUMmer3.19.tar.gz) = 54f3c692efb8bde7762c48186919754f2a8c178c
+Size (MUMmer3.19.tar.gz) = 3141991 bytes
+SHA1 (patch-aa) = e40b6538b259475def39cd8008af37d0a08e1555
 SHA1 (patch-ab) = af42da79fd287786cb83efa9c9b4fc8025abd728
 SHA1 (patch-ac) = 7f0f16bdd83bc80833f1ffdcfe1bad7c2ee76eec
 SHA1 (patch-ad) = 0804b2c966d7035c23444c4f72e1d93e45805bcf
diff --git a/biology/mummer/patches/patch-aa b/biology/mummer/patches/patch-aa
index 20723ca7f72..4f3836d2822 100644
--- a/biology/mummer/patches/patch-aa
+++ b/biology/mummer/patches/patch-aa
@@ -1,4 +1,4 @@
-$NetBSD: patch-aa,v 1.4 2006/12/06 16:52:20 joerg Exp $
+$NetBSD: patch-aa,v 1.5 2007/01/18 19:13:10 rillig 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 1.4 2006/12/06 16:52:20 joerg Exp $
  #-------------------------------------------------------------------------------
 -SHELL = /bin/sh
 +SHELL = ${SH}
- VERSION := 3.18
+ VERSION := 3.19
  
  
 @@ -35,15 +35,12 @@