diff options
author | schmonz <schmonz@pkgsrc.org> | 2009-04-21 17:51:05 +0000 |
---|---|---|
committer | schmonz <schmonz@pkgsrc.org> | 2009-04-21 17:51:05 +0000 |
commit | a6c1a37a8f3ee679cfaead457bfe3d2b2c629ec4 (patch) | |
tree | 46eb1e0e13568b5c30389faa5fcba71ca13cc5f7 /graphics/circos | |
parent | ebfb87ea8fb2c8f3b3b9e22d0b98a6236d473380 (diff) | |
download | pkgsrc-a6c1a37a8f3ee679cfaead457bfe3d2b2c629ec4.tar.gz |
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 (limited to 'graphics/circos')
-rw-r--r-- | graphics/circos/DESCR | 5 | ||||
-rw-r--r-- | graphics/circos/Makefile | 69 | ||||
-rw-r--r-- | graphics/circos/PLIST | 960 | ||||
-rw-r--r-- | graphics/circos/distinfo | 6 | ||||
-rw-r--r-- | graphics/circos/patches/patch-aa | 13 |
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 +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 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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", |