From 31bf4cc685eabdd5a5ffc0741946003a4a33a2e1 Mon Sep 17 00:00:00 2001 From: schmonz Date: Tue, 21 Apr 2009 17:51:05 +0000 Subject: 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 --- 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(+) create mode 100644 graphics/circos/DESCR create mode 100644 graphics/circos/Makefile create mode 100644 graphics/circos/PLIST create mode 100644 graphics/circos/distinfo create mode 100644 graphics/circos/patches/patch-aa (limited to 'graphics') 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 ${PKG_SYSCONFDIR}/fonts.conf + +SUBST_CLASSES+= paths +SUBST_STAGE.paths= do-configure +SUBST_FILES.paths= */*/*/circos*.conf bin/circos +SUBST_SED.paths+= -e 's|<>|<>|g' +SUBST_SED.paths+= -e 's|@PREFIX@|${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 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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", -- cgit v1.2.3