debian/0000755000000000000000000000000012146347177007202 5ustar debian/source/0000755000000000000000000000000012146347177010502 5ustar debian/source/format0000644000000000000000000000001411720203631011667 0ustar 3.0 (quilt) debian/copyright0000644000000000000000000001167512012676737011146 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: circos Source: http://circos.ca/distribution/circos-0.55.tgz Files: * Copyright: Copyright 2004-2011 Martin Krzywinski License: GPL-2+ Files: fonts/modern/* Copyright: 2005, Andrey V. Panov License: X11 with fonts exception Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, provided that the above copyright notice(s) and this permission notice appear in all copies of the Software and that both the above copyright notice(s) and this permission notice appear in supporting documentation. . THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT OF THIRD PARTY RIGHTS. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR HOLDERS INCLUDED IN THIS NOTICE BE LIABLE FOR ANY CLAIM, OR ANY SPECIAL INDIRECT OR CONSEQUENTIAL DAMAGES, OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. . Except as contained in this notice, the name of a copyright holder shall not be used in advertising or otherwise to promote the sale, use or other dealings in this Software without prior written authorization of the copyright holder. . As a special exception, if you create a document which uses these fonts, and embed these fonts or unaltered portions of these fonts into the document, these fonts does not by itself cause the resulting document to be covered by the X11 License. This exception does not however invalidate any other reasons why the document might be covered by the X11 License. If you modify these fonts, you may extend this exception to your version of the fonts, but you are not obligated to do so. If you do not wish to do so, delete this exception statement from your version. Comment: See http://bugs.debian.org/620537 Files: fonts/symbols/* Copyright: Copyright 2004-2011 Martin Krzywinski License: GPL-2+ Comment: See etc/conts.fonf: # All wingding and webding fonts have been replaced # by a GPL glyph font designed by Martin Krzywinski # for Circos. Files: etc/brewer.* Copyright: Cynthia A. Brewer, Mark Harrower, Pennsylvania State University License: Apache-2.0 Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at . http://www.apache.org/licenses/LICENSE-2.0 . Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License. Comment: On Debian systems, the complete text of the Apache License, Version 2.0 can be found in ‘/usr/share/common-licenses/Apache-2.0’. Files: debian/* Copyright: 2011 Olivier Sallou License: GPL-2+ This package is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. . This package is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. . You should have received a copy of the GNU General Public License along with this program. If not, see . On Debian systems, the complete text of the GNU General Public License version 2 can be found in "/usr/share/common-licenses/GPL-2". License: GPL-2+ This package is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. . This package is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. . You should have received a copy of the GNU General Public License along with this program. If not, see . On Debian systems, the complete text of the GNU General Public License version 2 can be found in "/usr/share/common-licenses/GPL-2". debian/compat0000644000000000000000000000000211720203631010357 0ustar 8 debian/watch0000644000000000000000000000016012146345257010225 0ustar version=3 opts=uversionmangle=s/\-/\./ http://circos.ca/software/download .*/distribution/circos-([-.\d]*)\.tgz debian/circos.examples0000644000000000000000000000001712146345257012217 0ustar example/* data debian/docs0000644000000000000000000000007011720203631010031 0ustar README README.tools README.tutorials fonts/README.fonts debian/circos.install0000644000000000000000000000013511720203631012032 0ustar bin/circos usr/bin/ etc/* etc/circos/ lib/* usr/share/perl5/ tiles/* usr/share/circos/tiles/ debian/circos.dirs0000644000000000000000000000002311720203631011321 0ustar usr/share/man/man1 debian/patches/0000755000000000000000000000000012146347177010631 5ustar debian/patches/fix_manpage0000644000000000000000000000106312146347076013030 0ustar Subject: fix errors from pod2man result Description: Perl file used as source for man page contains errors. Author: Olivier Sallou Last-Updated: 2013-05-20 Forwarded: No --- a/lib/Circos.pm +++ b/lib/Circos.pm @@ -7,7 +7,7 @@ =head1 NAME -Circos - Circular data visualizations for comparison of genomes, among other things +Circos \- Circular data visualizations for comparison of genomes, among other things =head1 SYNOPSIS @@ -6736,7 +6736,7 @@ =over -item * Hive plots +=item * Hive plots L debian/patches/use_ttf_fonts0000644000000000000000000000735612012676736013447 0ustar Author: Olivier Sallou Description: fonts-cmu use ttf, so update conf accordingly Last-Update: 2011-09-08 --- a/etc/fonts.conf +++ b/etc/fonts.conf @@ -27,18 +27,18 @@ # CMU Typewriter Regular, when rotated. For this reason, TTF versions # of these fonts are used. -serif = fonts/modern/cmunrm.otf # CMUSerif-Roman -serif_roman = fonts/modern/cmunrm.otf # CMUSerif-Roman -serif_default = fonts/modern/cmunrm.otf # CMUSerif-Roman -serif_normal = fonts/modern/cmunrm.otf # CMUSerif-Roman -serif_light = fonts/modern/cmunrm.otf # CMUSerif-Roman -serif_bold = fonts/modern/cmunbx.otf # CMUSerif-Bold -serif_italic = fonts/modern/cmunui.otf # CMUSerif-Italic -serif_bolditalic = fonts/modern/cmunbi.otf # CMUSerif-BoldItalic -serif_italicbold = fonts/modern/cmunbi.otf # CMUSerif-BoldItalic -serif_condensed = fonts/modern/cmunssdc.otf # CMUSerif-DemiCondensed -serif_condensedbold = fonts/modern/cmunssdc.otf # CMUSerif-DemiCondensed -serif_boldcondensed = fonts/modern/cmunssdc.otf # CMUSerif-DemiCondensed +serif = fonts/modern/cmunrm.ttf # CMUSerif-Roman +serif_roman = fonts/modern/cmunrm.ttf # CMUSerif-Roman +serif_default = fonts/modern/cmunrm.ttf # CMUSerif-Roman +serif_normal = fonts/modern/cmunrm.ttf # CMUSerif-Roman +serif_light = fonts/modern/cmunrm.ttf # CMUSerif-Roman +serif_bold = fonts/modern/cmunbx.ttf # CMUSerif-Bold +serif_italic = fonts/modern/cmunui.ttf # CMUSerif-Italic +serif_bolditalic = fonts/modern/cmunbi.ttf # CMUSerif-BoldItalic +serif_italicbold = fonts/modern/cmunbi.ttf # CMUSerif-BoldItalic +serif_condensed = fonts/modern/cmunssdc.ttf # CMUSerif-DemiCondensed +serif_condensedbold = fonts/modern/cmunssdc.ttf # CMUSerif-DemiCondensed +serif_boldcondensed = fonts/modern/cmunssdc.ttf # CMUSerif-DemiCondensed sans_serif = fonts/modern/cmunbmr.ttf # CMUBright-Roman sans = fonts/modern/cmunbmr.ttf # CMUBright-Roman @@ -46,20 +46,20 @@ light = fonts/modern/cmunbmr.ttf # CMUBright-Roman normal = fonts/modern/cmunbmr.ttf # CMUBright-Roman default = fonts/modern/cmunbmr.ttf # CMUBright-Roman -semibold = fonts/modern/cmunbsr.otf # CMUBright-Semibold -bold = fonts/modern/cmunbbx.otf # CMUBright-Bold -italic = fonts/modern/cmunbmo.otf # CMUBright-Oblique -bolditalic = fonts/modern/cmunbxo.otf # CMUBright-BoldOblique -italicbold = fonts/modern/cmunbxo.otf # CMUBright-BoldOblique +semibold = fonts/modern/cmunbsr.ttf # CMUBright-Semibold +bold = fonts/modern/cmunbbx.ttf # CMUBright-Bold +italic = fonts/modern/cmunbmo.ttf # CMUBright-Oblique +bolditalic = fonts/modern/cmunbxo.ttf # CMUBright-BoldOblique +italicbold = fonts/modern/cmunbxo.ttf # CMUBright-BoldOblique -condensed = fonts/modern/cmunssdc.otf # CMUSansSerif-DemiCondensed -condensedbold = fonts/modern/cmunssdc.otf # CMUSansSerif-DemiCondensed -boldcondensed = fonts/modern/cmunssdc.otf # CMUSansSerif-DemiCondensed +condensed = fonts/modern/cmunssdc.ttf # CMUSansSerif-DemiCondensed +condensedbold = fonts/modern/cmunssdc.ttf # CMUSansSerif-DemiCondensed +boldcondensed = fonts/modern/cmunssdc.ttf # CMUSansSerif-DemiCondensed mono = fonts/modern/cmuntt.ttf # CMUTypewriter-Regular fixed = fonts/modern/cmuntt.ttf # CMUTypewriter-Regular -mono_light = fonts/modern/cmunbtl.otf # CMUTypewriter-Light -fixed_light = fonts/modern/cmunbtl.otf # CMUTypewriter-Light +mono_light = fonts/modern/cmunbtl.ttf # CMUTypewriter-Light +fixed_light = fonts/modern/cmunbtl.ttf # CMUTypewriter-Light # All wingding and webding fonts have been replaced # by a GPL glyph font designed by Martin Krzywinski debian/patches/configpath_add_etc0000644000000000000000000000173012146346023014327 0ustar Description: Add Debian directories in search path Author: Olivier Sallou Last-Update: 2012-09-21 Forwarded: not-needed --- a/lib/Circos/Configuration.pm +++ b/lib/Circos/Configuration.pm @@ -693,6 +693,7 @@ } my @configpath = ( + "/etc/circos", dirname($file), dirname($file)."/etc", "$FindBin::RealBin/etc", --- a/etc/makehuesteps +++ b/etc/makehuesteps @@ -1,4 +1,4 @@ -#!/bin/env perl +#!/usr/bin/env perl use strict; use Math::Round qw(round); --- a/lib/Circos/Utils.pm +++ b/lib/Circos/Utils.pm @@ -441,7 +441,7 @@ # look for the file in various directories # v0.63 added configuration directory to dir_1 - my @dir_1 = grep($_,getcwd,Circos::Configuration::fetch_conf("configdir"),$FindBin::RealBin); + my @dir_1 = grep($_,getcwd,Circos::Configuration::fetch_conf("configdir"),$FindBin::RealBin,"/usr/share/circos"); my @dir_2 = qw(. .. ../.. ../../..); my @dir_3 = qw(. etc data); debian/patches/series0000644000000000000000000000011212146346341012030 0ustar use_ttf_fonts debianpackaging configpath_add_etc fix_examples fix_manpage debian/patches/fix_examples0000644000000000000000000000203112146345257013231 0ustar Subject: change path to conf file for examples Description: etc sub directory is hard coded in example conf files. In Debian conf files are in /etc/circos. This path is already added to search path. Author: Olivier Sallou Last-Updated: 2012-09-21 Forwarded: not-needed --- a/example/etc/circos.conf +++ b/example/etc/circos.conf @@ -248,16 +248,16 @@ <> -<> +<> -# includes etc/colors.conf -# etc/fonts.conf -# etc/patterns.conf -<> +# includes colors.conf +# fonts.conf +# patterns.conf +<> # system and debug settings -<> +<> anti_aliasing* = no --- a/example/run +++ b/example/run @@ -1,4 +1,4 @@ #!/bin/bash -../bin/circos -conf etc/circos.conf -debug_group summary,timer > run.out +circos -conf etc/circos.conf -debug_group summary,timer > run.out debian/patches/debianpackaging0000644000000000000000000000031011720203631013614 0ustar Description: Update env path Author: Olivier Sallou Last-Update: 2011-08-01 --- a/bin/circos +++ b/bin/circos @@ -1,4 +1,4 @@ -#!/bin/env perl +#!/usr/bin/env perl =pod debian/README.Debian0000644000000000000000000000077612012676737011254 0ustar Circos for Debian ----------------- To test the installation of the package, go to a copy of the directory /usr/share/doc/circos/example and execute: circos -conf circos.conf The files ‘circos.svg’ and ‘circos.png’ will be regenerated, and can be compared to the originals. Warning: Many example files are compressed in /usr/share/doc/circos/examples/*. Running the example program will failed due to the compressed files. To execute the sample program, you should first uncompress those files. debian/control0000644000000000000000000000432212012677304010574 0ustar Source: circos Section: science Priority: optional Maintainer: Debian Med Packaging Team Uploaders: Olivier Sallou , DM-Upload-Allowed: yes Build-Depends: debhelper (>= 8.0.0) Standards-Version: 3.9.3 Homepage: http://circos.ca/ Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/circos/trunk/ Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/circos/ Package: circos Architecture: all Pre-Depends: dpkg (>= 1.15.6) Depends: ${misc:Depends}, ${perl:Depends}, perl (>= 5.10), fonts-circos-symbols, fonts-cmu, libregexp-common-perl, libcarp-always-perl, libconfig-general-perl (>= 2.5), libdata-dumper-simple-perl, libgd-gd2-perl, libgetopt-simple-perl, libmath-bezier-perl, libmath-round-perl, libparams-validate-perl, libreadonly-perl, libset-intspan-perl (>= 1.16), liblist-allutils-perl, libfile-basedir-perl,libfile-spec-perl, libmath-bigint-perl,libmath-vec-perl, libio-all-perl, libmath-vecstat-perl, libgraphics-colorobject-perl, libtext-format-perl, libfont-ttf-perl, libclone-perl Recommends: circos-tools Description: plotter for visualizing data Circos visualizes data in a circular layout — ideal for exploring relationships between objects or positions, and creating highly informative publication-quality graphics. . This package provides the Circos plotting engine, which is command-line driven (like gnuplot) and fully scriptable. Package: otf-symbols-circos Pre-Depends: dpkg (>= 1.15.6) Depends: fonts-circos-symbols, ${misc:Depends} Architecture: all Section: oldlibs Priority: extra Description: transitional dummy package This package is a dummy transitional package. It can be safely removed. Package: fonts-circos-symbols Replaces: otf-symbols-circos (<< 0.61-2) Conflicts: otf-symbols-circos (<< 0.61-2) Provides: otf-symbols-circos Section: fonts Architecture: all Pre-Depends: dpkg (>= 1.15.6) Depends: ${misc:Depends} Description: plotter for visualizing data - standard fonts Circos visualizes data in a circular layout — ideal for exploring relationships between objects or positions, and creating highly informative publication-quality graphics. . This package provides a set of fonts used by default with Circos. debian/rules0000755000000000000000000000132011720203631010235 0ustar #!/usr/bin/make -f # -*- makefile -*- # debian/rules file for circos # Uncomment this to turn on verbose mode. #export DH_VERBOSE=1 %: dh $@ override_dh_install: dh_install # Update circos relative path to absolute debian paths find debian/circos -type f | xargs sed -i 's/include etc/include \/usr\/share\/circos\/etc/g' find debian/circos -type f | xargs sed -i 's/include fonts/include \/usr\/share\/circos\/fonts/g' find debian/circos -type f | xargs sed -i 's/include tiles/include \/usr\/share\/circos\/tiles/g' override_dh_installman: pod2man bin/circos > $(CURDIR)/debian/circos/usr/share/man/man1/circos.1 override_dh_builddeb: dh_builddeb -- -Z xz get-orig-source: bash debian/get-orig-source debian/fonts-circos-symbols.install0000644000000000000000000000004612012676737014670 0ustar fonts/symbols usr/share/circos/fonts/ debian/upstream0000644000000000000000000000122212012676737010761 0ustar Homepage: http://circos.ca/ Reference: Author: Martin I Krzywinski and Jacqueline E Schein and Inanc Birol and Joseph Connors and Randy Gascoyne and Doug Horsman and Steven J Jones and Marco A Marra Title: > Circos: An information aesthetic for comparative genomics Journal: Genome Research Year: 2009 Volume: 19 Number: 9 Pages: 1639-45 PMID: 19541911 DOI: 10.1101/gr.092759.109 URL: http://genome.cshlp.org/content/early/2009/06/15/gr.092759.109.abstract eprint: http://genome.cshlp.org/content/early/2009/06/15/gr.092759.109.full.pdf+html Repository: http://circos.ca/software/download/ Screenshots: http://circos.ca/tutorials/images/small/ debian/circos.links0000644000000000000000000000013311720203631011502 0ustar etc/circos usr/share/circos/etc usr/share/fonts/truetype/cmu usr/share/circos/fonts/modern debian/changelog0000644000000000000000000000266512146347121011052 0ustar circos (0.64-1) unstable; urgency=low * New upstream release -- Olivier Sallou Mon, 20 May 2013 09:01:27 +0200 circos (0.62.1-1) unstable; urgency=low * New upstream release -- Olivier Sallou Fri, 21 Sep 2012 17:00:12 +0200 circos (0.61-3) unstable; urgency=low * debian/control: add missing dependency (Closes: #684977). -- Olivier Sallou Wed, 15 Aug 2012 12:46:11 +0200 circos (0.61-2) unstable; urgency=low [ Olivier Sallou ] * debian/control: - Update description (Closes: #682802). - Rename otf-symbols-circos to fonts-circos-symbols to fit the Font Packages Naming Policy. - Move to Standards 3.9.3 -- Olivier Sallou Thu, 14 Jun 2012 13:46:15 +0200 circos (0.61-1) unstable; urgency=low [ Olivier Sallou ] * New upstream release [ Charles Plessy ] * renamed debian/upstream-metadata.yaml to debian/upstream [ Andreas Tille ] * debian/upstream: enhanced citation information -- Olivier Sallou Thu, 14 Jun 2012 12:56:33 +0200 circos (0.55-2) unstable; urgency=low * Add pre-depends on dpkg to support xz compression (required for Ubuntu) -- Olivier Sallou Wed, 19 Oct 2011 14:16:18 +0200 circos (0.55-1) unstable; urgency=low * First debian import (Closes: #632174) -- Olivier Sallou Wed, 29 Jun 2011 12:04:57 +0200