Initial import of graphics/circos.

Circos is a Perl application for the generation of publication-quality,
circularly composited renditions of genomic data and related annotations.

Circos is particularly suited for visualizing alignments, conservation and
intra and inter-chromosomal relationships.

Approved by: groo

5 files changed, 1053 insertions, 0 deletions

diff --git a/graphics/circos/DESCR b/graphics/circos/DESCR
new file mode 100644
index 00000000000..a9c4fd4c887
--- /dev/null
+++ b/graphics/circos/DESCR
@@ -0,0 +1,5 @@
+Circos is a Perl application for the generation of publication-quality,
+circularly composited renditions of genomic data and related annotations.
+
+Circos is particularly suited for visualizing alignments, conservation and
+intra and inter-chromosomal relationships.
diff --git a/graphics/circos/Makefile b/graphics/circos/Makefile
new file mode 100644
index 00000000000..26f559d083d
--- /dev/null
+++ b/graphics/circos/Makefile
@@ -0,0 +1,69 @@
+# $NetBSD: Makefile,v 1.1.1.1 2009/04/21 17:51:05 schmonz Exp $
+#
+
+DISTNAME=	circos-0.49
+CATEGORIES=	graphics
+MASTER_SITES=	http://mkweb.bcgsc.ca/circos/distribution/
+EXTRACT_SUFX=	.tgz
+
+MAINTAINER=	schmonz@NetBSD.org
+HOMEPAGE=	http://mkweb.bcgsc.ca/circos/
+COMMENT=	Concise, explanatory, unique and print-ready data visualization
+#LICENSE=
+
+USE_LANGUAGES=	# none
+USE_TOOLS+=	pax perl
+NO_BUILD=	yes
+
+DEPENDS+=	p5-Clone-[0-9]*:../../devel/p5-Clone
+DEPENDS+=	p5-Config-General-[0-9]*:../../devel/p5-Config-General
+DEPENDS+=	p5-GD-[0-9]*:../../graphics/p5-GD
+DEPENDS+=	p5-Math-Bezier-[0-9]*:../../math/p5-Math-Bezier
+DEPENDS+=	p5-Math-Round-[0-9]*:../../math/p5-Math-Round	# XXX commit
+DEPENDS+=	p5-Math-VecStat-[0-9]*:../../math/p5-Math-VecStat	# XXX
+DEPENDS+=	p5-Params-Validate-[0-9]*:../../devel/p5-Params-Validate
+DEPENDS+=	p5-Set-IntSpan>=1.11*:../../devel/p5-Set-IntSpan
+
+PKG_SYSCONFSUBDIR=	${PKGBASE}
+INSTALLATION_DIRS+=	bin share/${PKGBASE} ${FONTDIR} ${EGDIR}
+INSTALLATION_DIRS+=	share/doc/${PKGBASE}
+EGDIR=			share/examples/${PKGBASE}
+
+CONF_FILES+=		${EGDIR}/colors.conf ${PKG_SYSCONFDIR}/colors.conf
+CONF_FILES+=		${EGDIR}/fonts.conf ${PKG_SYSCONFDIR}/fonts.conf
+
+SUBST_CLASSES+=		paths
+SUBST_STAGE.paths=	do-configure
+SUBST_FILES.paths=	*/*/*/circos*.conf bin/circos
+SUBST_SED.paths+=	-e 's|<<include etc/\(.*\)>>|<<include ${PKG_SYSCONFDIR}/\1>>|g'
+SUBST_SED.paths+=	-e 's|@PREFIX@|${PREFIX}|g'
+
+REPLACE_PERL+=	data/3/make_random_highlights data/6/hist.random.make
+REPLACE_PERL+=	svg/textrotation.svg
+
+post-extract:
+	cd ${WRKSRC} && rm -f bin/${PKGBASE} \
+		&& mv bin/${PKGNAME_NOREV} bin/${PKGBASE}
+
+do-configure:
+	cd ${WRKSRC} && ( ${ECHO} ${PERL5:Q} ; ${ECHO} ) | ./install
+
+pre-configure:
+	cd ${WRKSRC} && rm -f bin/*.orig
+
+do-install:
+	cd ${WRKSRC} &&							\
+	for f in CHANGES README TODO; do				\
+		${INSTALL_DATA} $${f} ${PREFIX}/share/doc/${PKGBASE};	\
+	done;								\
+	for f in bin/*; do						\
+		${INSTALL_SCRIPT} $${f} ${PREFIX}/bin;			\
+	done;								\
+	for f in etc/*; do						\
+		${INSTALL_DATA} $${f} ${PREFIX}/${EGDIR};		\
+	done;								\
+	pax -rw -pp data fonts images svg tutorials ${PREFIX}/share/circos
+	# XXX install recursively data,images,svg,tutorials to share/circos
+	# XXX then see if stuff works, find more paths to fix
+
+.include "../../mk/bsd.pkg.mk"
diff --git a/graphics/circos/PLIST b/graphics/circos/PLIST
new file mode 100644
index 00000000000..15d4a04cdc6
--- /dev/null
+++ b/graphics/circos/PLIST
@@ -0,0 +1,960 @@
+@comment $NetBSD: PLIST,v 1.1.1.1 2009/04/21 17:51:05 schmonz Exp $
+bin/circos
+bin/gddiag
+share/circos/data/2/karyotype.all.txt
+share/circos/data/2/karyotype.dog.txt
+share/circos/data/2/karyotype.mouse.txt
+share/circos/data/2/karyotype.rat.txt
+share/circos/data/3/chr.hetero.highlights.txt
+share/circos/data/3/chr.highlights.colourless.txt
+share/circos/data/3/chr.highlights.txt
+share/circos/data/3/colors.txt
+share/circos/data/3/genes.cancer.txt
+share/circos/data/3/genes.formatted.txt
+share/circos/data/3/genes.omim.txt
+share/circos/data/3/genes.txt
+share/circos/data/3/h.variation.merged.txt
+share/circos/data/3/h.variation.txt
+share/circos/data/3/highlights.few.txt
+share/circos/data/3/make_random_highlights
+share/circos/data/3/random.highlights.3chrs.txt
+share/circos/data/3/random.highlights.r.txt
+share/circos/data/3/random.highlights.rr.txt
+share/circos/data/3/random.highlights.rrr.txt
+share/circos/data/3/random.highlights.txt
+share/circos/data/3/random.highlights.z_by_size.txt
+share/circos/data/3/random.highlights.zr_by_size.txt
+share/circos/data/5/curves.repeated.txt
+share/circos/data/5/curves.txt
+share/circos/data/5/ribbon.twist.txt
+share/circos/data/5/ribbon.txt
+share/circos/data/5/segdup.bundle1.txt
+share/circos/data/5/segdup.bundle2.txt
+share/circos/data/5/segdup.bundle3.colored.txt
+share/circos/data/5/segdup.bundle3.txt
+share/circos/data/5/segdup.bundle4.txt
+share/circos/data/5/segdup.bundle5.txt
+share/circos/data/5/segdup.short.txt
+share/circos/data/5/segdup.txt
+share/circos/data/6/assembly.txt
+share/circos/data/6/connectors.txt
+share/circos/data/6/conservation.avg.txt
+share/circos/data/6/conservation.p5.txt
+share/circos/data/6/conservation.p95.txt
+share/circos/data/6/conservation.txt
+share/circos/data/6/epi.tmp.txt
+share/circos/data/6/epi.txt
+share/circos/data/6/gene.density
+share/circos/data/6/gene.density.txt
+share/circos/data/6/genes.exons.txt
+share/circos/data/6/genes.glyph.txt
+share/circos/data/6/genes.txt
+share/circos/data/6/highlights.txt
+share/circos/data/6/hist.random.2.txt
+share/circos/data/6/hist.random.3.txt
+share/circos/data/6/hist.random.4.txt
+share/circos/data/6/hist.random.5.txt
+share/circos/data/6/hist.random.make
+share/circos/data/6/hist.random.txt
+share/circos/data/6/histogram.neg.txt
+share/circos/data/6/histogram.pos.txt
+share/circos/data/6/histogram.txt
+share/circos/data/6/histogram.uneven.txt
+share/circos/data/6/rand.1.txt
+share/circos/data/6/rand.2.txt
+share/circos/data/6/rand.3.txt
+share/circos/data/6/rand.4.txt
+share/circos/data/6/segdup.txt
+share/circos/data/6/sequence.long.txt
+share/circos/data/6/sequence.txt
+share/circos/data/6/snp.density.1mb.txt
+share/circos/data/6/snp.density.250kb.txt
+share/circos/data/6/snp.density.25kb.txt
+share/circos/data/6/snp.density.500kb.txt
+share/circos/data/6/snp.density.50kb.txt
+share/circos/data/6/snp.density.txt
+share/circos/data/6/snp.number.1mb.txt
+share/circos/data/6/snp.number.250kb.txt
+share/circos/data/6/snp.number.25kb.txt
+share/circos/data/6/snp.number.500kb.txt
+share/circos/data/6/snp.number.50kb.txt
+share/circos/data/6/text.100labels.txt
+share/circos/data/6/text.genes.txt
+share/circos/data/6/text.genes.znf.txt
+share/circos/data/6/tiles.rand.1.txt
+share/circos/data/6/variation.heatmap.txt
+share/circos/data/6/variation.txt
+share/circos/data/7/heatmap.zoom-01.txt
+share/circos/data/7/heatmap.zoom-02.txt
+share/circos/data/7/heatmap.zoom-03.txt
+share/circos/data/7/heatmap.zoom-04.txt
+share/circos/data/7/heatmap.zoom-05.txt
+share/circos/data/7/heatmap.zoom-06.txt
+share/circos/data/7/karyotype.human.colorbychr.txt
+share/circos/data/8/background.png
+share/circos/data/8/chr1-random.txt
+share/circos/data/8/chrall-random.txt
+share/circos/data/8/circos-microbe-data.tgz
+share/circos/data/8/histogram.stacked.txt
+share/circos/data/8/histogram.txt
+share/circos/data/8/karyotype.microbe.txt
+share/circos/data/8/microbe.highlights.1.txt
+share/circos/data/8/microbe.highlights.10.txt
+share/circos/data/8/microbe.highlights.11.txt
+share/circos/data/8/microbe.highlights.12.txt
+share/circos/data/8/microbe.highlights.13.txt
+share/circos/data/8/microbe.highlights.14.txt
+share/circos/data/8/microbe.highlights.15.txt
+share/circos/data/8/microbe.highlights.16.txt
+share/circos/data/8/microbe.highlights.17.txt
+share/circos/data/8/microbe.highlights.18.txt
+share/circos/data/8/microbe.highlights.19.txt
+share/circos/data/8/microbe.highlights.2.labels.1.txt
+share/circos/data/8/microbe.highlights.2.labels.2.txt
+share/circos/data/8/microbe.highlights.2.labels.3.txt
+share/circos/data/8/microbe.highlights.2.txt
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+share/circos/data/8/microbe.highlights.21.txt
+share/circos/data/8/microbe.highlights.22.txt
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+share/circos/data/8/microbe.highlights.24.txt
+share/circos/data/8/microbe.highlights.25.txt
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+share/circos/data/8/microbe.highlights.7.txt
+share/circos/data/8/microbe.highlights.8.txt
+share/circos/data/8/microbe.highlights.9.txt
+share/circos/data/8/microbe.labels.2.txt
+share/circos/data/8/microbe.labels.txt
+share/circos/data/8/microbe.plot.1.txt
+share/circos/data/8/microbe.plot.2.txt
+share/circos/data/8/microbe.plot.3.txt
+share/circos/data/8/microbe.separator.txt
+share/circos/data/8/microbe.sequence.txt
+share/circos/data/8/microbe.tile.txt
+share/circos/data/8/text.bands.txt
+share/circos/data/karyotype.human.colorbychr.txt
+share/circos/data/karyotype.human.txt
+share/circos/data/text.bands.txt
+share/circos/fonts/frutiger55.ttf
+share/circos/fonts/frutiger57.ttf
+share/circos/fonts/frutiger65.ttf
+share/circos/fonts/frutiger67.ttf
+share/circos/fonts/LTe50046.ttf
+share/circos/fonts/LTe50048.ttf
+share/circos/fonts/LTe50050.ttf
+share/circos/fonts/LTe50054.ttf
+share/circos/fonts/lucon.svg
+share/circos/fonts/lucon.ttf
+share/circos/fonts/pragmata.ttf
+share/circos/fonts/wingding.ttf
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+share/circos/tutorials/7/3/circos.conf
+share/circos/tutorials/7/3/ideogram.conf
+share/circos/tutorials/7/3/image-01.png
+share/circos/tutorials/7/3/image-02.png
+share/circos/tutorials/7/3/image-03.png
+share/circos/tutorials/7/3/image-04.png
+share/circos/tutorials/7/3/ticks.conf
+share/circos/tutorials/7/4/circos.conf
+share/circos/tutorials/7/4/ideogram.conf
+share/circos/tutorials/7/4/image-01.png
+share/circos/tutorials/7/4/ticks.conf
+share/circos/tutorials/7/5/circos.conf
+share/circos/tutorials/7/5/ideogram.conf
+share/circos/tutorials/7/5/image-01.png
+share/circos/tutorials/7/5/image-02.png
+share/circos/tutorials/7/5/image-03.png
+share/circos/tutorials/7/5/ticks.conf
+share/circos/tutorials/7/6/circos.conf
+share/circos/tutorials/7/6/ideogram.conf
+share/circos/tutorials/7/6/image-01.png
+share/circos/tutorials/7/6/image-02.png
+share/circos/tutorials/7/6/image-03.png
+share/circos/tutorials/7/6/image-04.png
+share/circos/tutorials/7/6/ticks.conf
+share/circos/tutorials/7/7/circos.conf
+share/circos/tutorials/7/7/ideogram.conf
+share/circos/tutorials/7/7/image-01.png
+share/circos/tutorials/7/7/image-02.png
+share/circos/tutorials/7/7/ticks.conf
+share/circos/tutorials/7/image-prep.png
+share/circos/tutorials/7/image.png
+share/circos/tutorials/8/1/circos-microbe-sample.tgz
+share/circos/tutorials/8/1/circos.conf
+share/circos/tutorials/8/1/ideogram.conf
+share/circos/tutorials/8/1/image-01.png
+share/circos/tutorials/8/1/image-02.png
+share/circos/tutorials/8/1/image-03.png
+share/circos/tutorials/8/1/ticks.conf
+share/circos/tutorials/8/2/circos.conf
+share/circos/tutorials/8/2/circos.image-01.conf
+share/circos/tutorials/8/2/circos.image-02.conf
+share/circos/tutorials/8/2/circos.image-03.conf
+share/circos/tutorials/8/2/circos.image-04.conf
+share/circos/tutorials/8/2/circos.image-05.conf
+share/circos/tutorials/8/2/circos.image-06.conf
+share/circos/tutorials/8/2/circos.image-07.conf
+share/circos/tutorials/8/2/ideogram.conf
+share/circos/tutorials/8/2/image-01.png
+share/circos/tutorials/8/2/image-02.png
+share/circos/tutorials/8/2/image-03.png
+share/circos/tutorials/8/2/image-04.png
+share/circos/tutorials/8/2/image-05.png
+share/circos/tutorials/8/2/image-06.png
+share/circos/tutorials/8/2/image-07.png
+share/circos/tutorials/8/2/image-08.png
+share/circos/tutorials/8/2/ticks.conf
+share/circos/tutorials/8/3/circos.conf
+share/circos/tutorials/8/3/ideogram.conf
+share/circos/tutorials/8/3/image-01.png
+share/circos/tutorials/8/3/image-02.png
+share/circos/tutorials/8/3/ticks.conf
+share/circos/tutorials/8/4/imagemap.txt
+share/circos/tutorials/8/5/circos.conf
+share/circos/tutorials/8/5/ideogram.conf
+share/circos/tutorials/8/5/image-01.png
+share/circos/tutorials/8/5/image-02.png
+share/circos/tutorials/8/5/image-03.png
+share/circos/tutorials/8/5/image-04.png
+share/circos/tutorials/8/5/image-05.png
+share/circos/tutorials/8/5/image-06.png
+share/circos/tutorials/8/5/image-07.png
+share/circos/tutorials/8/5/ticks.conf
+share/circos/tutorials/8/6/circos.conf
+share/circos/tutorials/8/6/ideogram.conf
+share/circos/tutorials/8/6/image-01.png
+share/circos/tutorials/8/6/image-02.png
+share/circos/tutorials/8/6/image-03.png
+share/circos/tutorials/8/6/image-04.png
+share/circos/tutorials/8/6/ticks.conf
+share/circos/tutorials/8/7/circos.conf
+share/circos/tutorials/8/7/ideogram.conf
+share/circos/tutorials/8/7/image-01.png
+share/circos/tutorials/8/7/ticks.conf
+share/circos/tutorials/8/8/circos.conf
+share/circos/tutorials/8/8/ideogram.conf
+share/circos/tutorials/8/8/image-01.png
+share/circos/tutorials/8/8/image-02.png
+share/circos/tutorials/8/8/image-03.png
+share/circos/tutorials/8/8/image-04.png
+share/circos/tutorials/8/8/ticks.conf
+share/circos/tutorials/8/9/circos.conf
+share/circos/tutorials/8/9/ideogram.conf
+share/circos/tutorials/8/9/image-01.png
+share/circos/tutorials/8/9/image-02.png
+share/circos/tutorials/8/9/image-03.png
+share/circos/tutorials/8/9/image-04.png
+share/circos/tutorials/8/9/image-05.png
+share/circos/tutorials/8/9/randomlinks.conf
+share/circos/tutorials/8/9/ticks.conf
+share/circos/tutorials/8/image.png
+share/circos/tutorials/9/1/image-01.png
+share/circos/tutorials/9/2/eq.eps
+share/circos/tutorials/9/2/image-01.png
+share/circos/tutorials/9/2/image-02.png
+share/circos/tutorials/9/2/image-03.png
+share/circos/tutorials/9/2/image-04.png
+share/circos/tutorials/9/2/image-05.png
+share/circos/tutorials/9/2/image-06.png
+share/circos/tutorials/9/3/image-01.png
+share/circos/tutorials/9/3/image-02.png
+share/circos/tutorials/9/3/image-03.png
+share/circos/tutorials/9/3/image-04.png
+share/circos/tutorials/9/3/image-05.png
+share/circos/tutorials/9/3/image-06.png
+share/circos/tutorials/9/5/image-00.png
+share/circos/tutorials/9/5/image-01.png
+share/circos/tutorials/9/5/image-03.png
+share/circos/tutorials/9/5/image-04.png
+share/circos/tutorials/9/5/image-05.png
+share/circos/tutorials/9/5/image-06.png
+share/circos/tutorials/9/5/image-07.png
+share/circos/tutorials/9/image.png
+share/doc/circos/CHANGES
+share/doc/circos/README
+share/doc/circos/TODO
+share/examples/circos/colors.conf
+share/examples/circos/fonts.conf
+@dirrm share/examples/circos
+@dirrm share/doc/circos
+@dirrm share/circos/tutorials/9/5
+@dirrm share/circos/tutorials/9/4
+@dirrm share/circos/tutorials/9/3
+@dirrm share/circos/tutorials/9/2
+@dirrm share/circos/tutorials/9/1
+@dirrm share/circos/tutorials/9
+@dirrm share/circos/tutorials/8/9
+@dirrm share/circos/tutorials/8/8
+@dirrm share/circos/tutorials/8/7
+@dirrm share/circos/tutorials/8/6
+@dirrm share/circos/tutorials/8/5
+@dirrm share/circos/tutorials/8/4
+@dirrm share/circos/tutorials/8/3
+@dirrm share/circos/tutorials/8/2
+@dirrm share/circos/tutorials/8/1
+@dirrm share/circos/tutorials/8
+@dirrm share/circos/tutorials/7/7
+@dirrm share/circos/tutorials/7/6
+@dirrm share/circos/tutorials/7/5
+@dirrm share/circos/tutorials/7/4
+@dirrm share/circos/tutorials/7/3
+@dirrm share/circos/tutorials/7/2
+@dirrm share/circos/tutorials/7/1
+@dirrm share/circos/tutorials/7
+@dirrm share/circos/tutorials/6/9
+@dirrm share/circos/tutorials/6/8
+@dirrm share/circos/tutorials/6/7
+@dirrm share/circos/tutorials/6/6
+@dirrm share/circos/tutorials/6/5
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+@dirrm share/circos/tutorials/6/3
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+@dirrm share/circos/tutorials/6/11
+@dirrm share/circos/tutorials/6/10
+@dirrm share/circos/tutorials/6/1
+@dirrm share/circos/tutorials/6
+@dirrm share/circos/tutorials/5/9
+@dirrm share/circos/tutorials/5/8
+@dirrm share/circos/tutorials/5/7
+@dirrm share/circos/tutorials/5/6
+@dirrm share/circos/tutorials/5/5
+@dirrm share/circos/tutorials/5/4
+@dirrm share/circos/tutorials/5/3
+@dirrm share/circos/tutorials/5/2
+@dirrm share/circos/tutorials/5/10
+@dirrm share/circos/tutorials/5/1
+@dirrm share/circos/tutorials/5
+@dirrm share/circos/tutorials/4/9
+@dirrm share/circos/tutorials/4/8
+@dirrm share/circos/tutorials/4/7
+@dirrm share/circos/tutorials/4/6
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+@dirrm share/circos/tutorials/4/3
+@dirrm share/circos/tutorials/4/2
+@dirrm share/circos/tutorials/4/1
+@dirrm share/circos/tutorials/4
+@dirrm share/circos/tutorials/3/9
+@dirrm share/circos/tutorials/3/8
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+@dirrm share/circos/tutorials/2/9
+@dirrm share/circos/tutorials/2/8
+@dirrm share/circos/tutorials/2/7
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+@dirrm share/circos/tutorials/2/5
+@dirrm share/circos/tutorials/2/4
+@dirrm share/circos/tutorials/2/3
+@dirrm share/circos/tutorials/2/2
+@dirrm share/circos/tutorials/2/10
+@dirrm share/circos/tutorials/2/1
+@dirrm share/circos/tutorials/2
+@dirrm share/circos/tutorials/1/8
+@dirrm share/circos/tutorials/1/7
+@dirrm share/circos/tutorials/1/6
+@dirrm share/circos/tutorials/1/5
+@dirrm share/circos/tutorials/1/4
+@dirrm share/circos/tutorials/1/3
+@dirrm share/circos/tutorials/1/2
+@dirrm share/circos/tutorials/1/1
+@dirrm share/circos/tutorials/1
+@dirrm share/circos/tutorials
+@dirrm share/circos/svg
+@dirrm share/circos/images/3000px
+@dirrm share/circos/images/250px
+@dirrm share/circos/images/100px
+@dirrm share/circos/images
+@dirrm share/circos/fonts
+@dirrm share/circos/data/8
+@dirrm share/circos/data/7
+@dirrm share/circos/data/6
+@dirrm share/circos/data/5
+@dirrm share/circos/data/3
+@dirrm share/circos/data/2
+@dirrm share/circos/data
+@dirrm share/circos
diff --git a/graphics/circos/distinfo b/graphics/circos/distinfo
new file mode 100644
index 00000000000..1052b2c8c12
--- /dev/null
+++ b/graphics/circos/distinfo
@@ -0,0 +1,6 @@
+$NetBSD: distinfo,v 1.1.1.1 2009/04/21 17:51:05 schmonz Exp $
+
+SHA1 (circos-0.49.tgz) = 04cbdd25ba86104d2f68d5feb611f37ddc409bca
+RMD160 (circos-0.49.tgz) = 00f2d9913530781849a2ea48097eb05a5824f0c4
+Size (circos-0.49.tgz) = 73468067 bytes
+SHA1 (patch-aa) = 4a6dc1be8b3c57a9a6c2a31fd67b6f09aebf6cc5
diff --git a/graphics/circos/patches/patch-aa b/graphics/circos/patches/patch-aa
new file mode 100644
index 00000000000..eb274ea2d8f
--- /dev/null
+++ b/graphics/circos/patches/patch-aa
@@ -0,0 +1,13 @@
+$NetBSD: patch-aa,v 1.1.1.1 2009/04/21 17:51:05 schmonz Exp $
+
+--- bin/circos.orig	2009-01-30 18:31:20.000000000 -0500
++++ bin/circos
+@@ -317,6 +317,8 @@ use vars qw(%OPT %CONF);
+ #print Dumper(\%INC);
+ #exit;
+ 
++chdir "@PREFIX@/share/circos" || die "error - cannot chdir";
++
+ GetOptions(\%OPT,
+ 	   "imagemap",
+ 	   "silent",