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[pkgsrc/trunk]: pkgsrc/graphics/circos Initial import of graphics/circos.
details: https://anonhg.NetBSD.org/pkgsrc/rev/50a208cbafc4
branches: trunk
changeset: 391902:50a208cbafc4
user: schmonz <schmonz%pkgsrc.org@localhost>
date: Tue Apr 21 17:51:05 2009 +0000
description:
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
diffstat:
graphics/circos/DESCR | 5 +
graphics/circos/Makefile | 69 ++
graphics/circos/PLIST | 960 +++++++++++++++++++++++++++++++++++++++
graphics/circos/distinfo | 6 +
graphics/circos/patches/patch-aa | 13 +
5 files changed, 1053 insertions(+), 0 deletions(-)
diffs (truncated from 1073 to 300 lines):
diff -r 4fa77c10b8a2 -r 50a208cbafc4 graphics/circos/DESCR
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/graphics/circos/DESCR Tue Apr 21 17:51:05 2009 +0000
@@ -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 -r 4fa77c10b8a2 -r 50a208cbafc4 graphics/circos/Makefile
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/graphics/circos/Makefile Tue Apr 21 17:51:05 2009 +0000
@@ -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@localhost
+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 -r 4fa77c10b8a2 -r 50a208cbafc4 graphics/circos/PLIST
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/graphics/circos/PLIST Tue Apr 21 17:51:05 2009 +0000
@@ -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
+share/circos/data/8/microbe.highlights.20.txt
+share/circos/data/8/microbe.highlights.21.txt
+share/circos/data/8/microbe.highlights.22.txt
+share/circos/data/8/microbe.highlights.23.txt
+share/circos/data/8/microbe.highlights.24.txt
+share/circos/data/8/microbe.highlights.25.txt
+share/circos/data/8/microbe.highlights.26.txt
+share/circos/data/8/microbe.highlights.4.txt
+share/circos/data/8/microbe.highlights.5.txt
+share/circos/data/8/microbe.highlights.6.txt
+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
+share/circos/images/100px/tutorial-01-02.png
+share/circos/images/100px/tutorial-02-02.png
+share/circos/images/100px/tutorial-02-03.png
+share/circos/images/100px/tutorial-02-04.png
+share/circos/images/100px/tutorial-02-05.png
+share/circos/images/100px/tutorial-02-06.png
+share/circos/images/100px/tutorial-02-07.png
+share/circos/images/100px/tutorial-02-08.png
+share/circos/images/100px/tutorial-02-09.png
+share/circos/images/100px/tutorial-02-10.png
+share/circos/images/100px/tutorial-03-01.png
+share/circos/images/100px/tutorial-03-02.png
+share/circos/images/100px/tutorial-03-03.png
+share/circos/images/100px/tutorial-03-04.png
+share/circos/images/100px/tutorial-03-05.png
+share/circos/images/100px/tutorial-03-06.png
+share/circos/images/100px/tutorial-03-07.png
+share/circos/images/100px/tutorial-03-08.png
+share/circos/images/100px/tutorial-03-09.png
+share/circos/images/100px/tutorial-04-01.png
+share/circos/images/100px/tutorial-04-02.png
+share/circos/images/100px/tutorial-04-03.png
+share/circos/images/100px/tutorial-04-04.png
+share/circos/images/100px/tutorial-04-05.png
+share/circos/images/100px/tutorial-04-06.png
+share/circos/images/100px/tutorial-04-07.png
+share/circos/images/100px/tutorial-04-08.png
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+share/circos/images/100px/tutorial-05-03.png
+share/circos/images/100px/tutorial-05-04.png
+share/circos/images/100px/tutorial-05-05.png
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+share/circos/images/100px/tutorial-05-10.png
+share/circos/images/100px/tutorial-06-01.png
+share/circos/images/100px/tutorial-06-02.png
+share/circos/images/100px/tutorial-06-03.png
+share/circos/images/100px/tutorial-06-04.png
+share/circos/images/100px/tutorial-06-05.png
+share/circos/images/100px/tutorial-06-06.png
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+share/circos/images/100px/tutorial-06-10.png
+share/circos/images/100px/tutorial-06-11.png
+share/circos/images/100px/tutorial-07-01.png
+share/circos/images/100px/tutorial-07-02.png
+share/circos/images/100px/tutorial-07-03.png
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+share/circos/images/100px/tutorial-08-05.png
+share/circos/images/100px/tutorial-08-06.png
+share/circos/images/100px/tutorial-08-07.png
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