[med-svn] r7187 - in trunk/packages/circos/trunk: . debian debian/patches debian/source
olivier sallou
osallou-guest at alioth.debian.org
Thu Jun 30 11:32:37 UTC 2011
Author: osallou-guest
Date: 2011-06-30 11:32:37 +0000 (Thu, 30 Jun 2011)
New Revision: 7187
Added:
trunk/packages/circos/trunk/debian/
trunk/packages/circos/trunk/debian/README
trunk/packages/circos/trunk/debian/README.source
trunk/packages/circos/trunk/debian/changelog
trunk/packages/circos/trunk/debian/circos-tutorials.install
trunk/packages/circos/trunk/debian/circos.install
trunk/packages/circos/trunk/debian/circos.links
trunk/packages/circos/trunk/debian/compat
trunk/packages/circos/trunk/debian/control
trunk/packages/circos/trunk/debian/copyright
trunk/packages/circos/trunk/debian/docs
trunk/packages/circos/trunk/debian/patches/
trunk/packages/circos/trunk/debian/patches/debianpackaging
trunk/packages/circos/trunk/debian/patches/series
trunk/packages/circos/trunk/debian/rules
trunk/packages/circos/trunk/debian/source/
trunk/packages/circos/trunk/debian/source/format
trunk/packages/circos/trunk/debian/watch
Log:
[svn-inject] Applying Debian modifications (0.54.1-1) to trunk
Property changes on: trunk/packages/circos/trunk/debian
___________________________________________________________________
Added: mergeWithUpstream
+ 1
Added: trunk/packages/circos/trunk/debian/README
===================================================================
--- trunk/packages/circos/trunk/debian/README (rev 0)
+++ trunk/packages/circos/trunk/debian/README 2011-06-30 11:32:37 UTC (rev 7187)
@@ -0,0 +1,150 @@
+
+ / ___(_)_ __ ___ ___ __
+ | | | | '__/ __/ _ \/ __|
+ | |___| | | | (_| (_) \__ \
+ \____|_|_| \___\___/|___/
+
+ round is good
+
+################################################################
+
+Circos - circular genome data and annotation image generator
+
+Martin Krzywinski
+Canada's Michael Smith Genome Sciences Center
+British Columbia Cancer Agency
+
+martink at bcgsc.ca
+mkweb.bcgsc.ca/circos
+
+################################################################
+
+0. INTRODUCTION
+ 0.a what is circos?
+
+1. GETTING STARTED
+
+2. BUGS
+ 2.a known issues
+
+3. OTHER ISSUES
+ 3.a typical errors and how to fix them
+ 3.a.1 numerical parameter units
+
+################################################################
+
+0. INTRODUCTION
+
+0.a what is circos?
+
+Circos is a program 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.
+
+But wait. Also, Circos is useful to visualize any type of information
+that benefits from a circular layout. Thus, although it has been
+designed for the field of genomics, it is sufficiently flexible to be
+used in other data domains.
+
+Circos supports TTF fonts. A few fonts are included in /usr/share/circos/fonts/.
+
+1. GETTING STARTED
+
+Now try creating an image from one of the tutorials.
+
+> circos -conf /usr/share/circos/tutorials/2/2/circos.conf
+
+If everything goes well, the program should terminate with a line
+
+ created image at /tmp/circos-tutorial.png
+
+To get some verbose reporting, use
+
+> circos -conf /usr/share/circos/tutorials/2/2/circos.conf -debug
+
+Please see mkweb.bcgsc.ca/circos for documentation. There are a large number
+of tutorials that described how the configuration files are formatted.
+
+1.b tools
+
+There are several helper scripts located in tools/ that are designed
+to aid you in processing your data.
+
+Many of these involve manipulating link files. These tools independent
+scripts and are covered in Tutorial 9.
+
+ http://mkweb.bcgsc.ca/circos/?tutorials&id=9
+
+
+2. BUGS
+
+2.a known issues
+
+GD does not draw rotated text correctly when the font size is small. For example,
+using a font size of 6pt, text drawn an an angle is drawn with letters upright. If you
+see this, increase the font size of the text.
+
+3. OTHER ISSUES
+
+3.a typical errors and how to fix them
+
+3.a.1 numerical parameter units
+
+Many numerical parameters in the .conf files require that you specify
+a unit. For a given parameter, one or more of these units may be required
+
+ p - absolute size in pixels
+ r - relative size, with the comparator being context sensitive
+ e.g. relative tick size is relative to ideogram thickness
+ e.g. relative tick label offset is relative to tick size
+ u - chromosome units, as defined by chromosomes_unit
+ b - bases, the natural unit along the ideogram
+ n - no unit, explicitly stated
+
+If you receive an error message of the kind
+
+The parameter [ideogram/spacing/break_style/thickness] value [0.25] does not have
+ the correct unit [saw n], which should be one of r,p at bin/circos line 3410
+ main::unit_validate(0.25, 'ideogram/spacing/break_style/thickness', 'r', 'p') called atbin/circos line 3559
+ main::draw_axis_break('HASH(0x8a81d10)') called at bin/circos line 872
+
+Then you have the wrong unit. Here the parameter at fault is
+
+ ideogram/spacing/break_style/thickness
+
+that is
+
+ <ideogram>
+ <spacing>
+ <break_style>
+ thickness =
+
+It is defined to be 0.25 (no unit) but requires that it have a unit of
+either "r" (relative) or "p" (absolute).
+
+As Circos matures, and the configuration file syntax stabilizes, I am
+striving to standardize the requirement for units for all
+parameters. Previous versions were more tolerant and attempted to
+naively determine the unit automatically (e.g. if value was <1 then
+the unit was assumed relative) and you may find that after upgrading
+to a new version of Circos your old files are creating errors. Just
+add the units and you're good to go.
+
+3.a.2 no text in figures
+
+If Circos is creating images, but without any text (ideogram labels,
+tick labels, etc), it is almost certain that your GD Perl module was
+compiled without True Type support.
+
+See the note about gddiag above.
+
+This may be due to the fact that you don't have the True Type library
+on your system (freetype), or a configuration error during GD
+installation.
+
+You'll need to reinstall GD.
+
+http://search.cpan.org/dist/GD/
Added: trunk/packages/circos/trunk/debian/README.source
===================================================================
--- trunk/packages/circos/trunk/debian/README.source (rev 0)
+++ trunk/packages/circos/trunk/debian/README.source 2011-06-30 11:32:37 UTC (rev 7187)
@@ -0,0 +1,7 @@
+circos for Debian
+-----------------
+
+Remote upstream files (tar.gz) are delivered as full package when named xxx-dd.tar.gz, but patches named xxx-dd-pp.tar.gz contains only modified files. As such, watch/uscan cannot be used for automated update of upstream code. Major delivery should be downloaded, then latest patch should overwrite files.
+
+
+
Added: trunk/packages/circos/trunk/debian/changelog
===================================================================
--- trunk/packages/circos/trunk/debian/changelog (rev 0)
+++ trunk/packages/circos/trunk/debian/changelog 2011-06-30 11:32:37 UTC (rev 7187)
@@ -0,0 +1,5 @@
+circos (0.54.1-1) unstable; urgency=low
+
+ * First debian import (Closes: #632174)
+
+ -- Olivier Sallou <olivier.sallou at irisa.fr> Wed, 29 Jun 2011 12:04:57 +0200
Added: trunk/packages/circos/trunk/debian/circos-tutorials.install
===================================================================
--- trunk/packages/circos/trunk/debian/circos-tutorials.install (rev 0)
+++ trunk/packages/circos/trunk/debian/circos-tutorials.install 2011-06-30 11:32:37 UTC (rev 7187)
@@ -0,0 +1 @@
+tutorials/* usr/share/circos/tutorials/
Added: trunk/packages/circos/trunk/debian/circos.install
===================================================================
--- trunk/packages/circos/trunk/debian/circos.install (rev 0)
+++ trunk/packages/circos/trunk/debian/circos.install 2011-06-30 11:32:37 UTC (rev 7187)
@@ -0,0 +1,7 @@
+bin/circos usr/bin/
+data/* var/lib/circos/data/
+etc/* etc/circos/
+fonts/* usr/share/circos/fonts/
+lib/* usr/lib/perl5/
+svg/* usr/share/circos/svg/
+tiles/* usr/share/circos/tiles/
Added: trunk/packages/circos/trunk/debian/circos.links
===================================================================
--- trunk/packages/circos/trunk/debian/circos.links (rev 0)
+++ trunk/packages/circos/trunk/debian/circos.links 2011-06-30 11:32:37 UTC (rev 7187)
@@ -0,0 +1 @@
+etc/circos usr/share/circos/etc
Added: trunk/packages/circos/trunk/debian/compat
===================================================================
--- trunk/packages/circos/trunk/debian/compat (rev 0)
+++ trunk/packages/circos/trunk/debian/compat 2011-06-30 11:32:37 UTC (rev 7187)
@@ -0,0 +1 @@
+8
Added: trunk/packages/circos/trunk/debian/control
===================================================================
--- trunk/packages/circos/trunk/debian/control (rev 0)
+++ trunk/packages/circos/trunk/debian/control 2011-06-30 11:32:37 UTC (rev 7187)
@@ -0,0 +1,29 @@
+Source: circos
+Section: science
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Olivier Sallou <olivier.sallou at irisa.fr>,
+DM-Upload-Allowed: yes
+Build-Depends: debhelper (>= 8.0.0)
+Standards-Version: 3.9.2
+Homepage: http://circos.ca/
+Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/circos/trunk/
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/circos/?rev=0&sc=0
+
+Package: circos
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}, ${perl:Depends}, perl (>= 5.10), libregexp-common-perl, libcarp-always-perl, libconfig-general-perl, libdata-dumper-simple-perl, libgd-gd2-perl, libgetopt-simple-perl, libmath-bezier-perl, libmath-round-perl, libparams-validate-perl, libreadonly-perl, libset-intspan-perl, liblist-allutils-perl, libfile-basedir-perl,libfile-spec-perl, libmath-bigint-perl,libmath-vec-perl, libio-all-perl
+Suggests: circos-tools
+Description: Package for visualizing data and information
+ It visualizes data in a circular layout — this makes Circos
+ ideal for exploring relationships between objects or positions.
+ Circos is ideal for creating publication-quality infographics
+ and illustrations with a high data-to-ink ratio, richly layered
+ data and pleasant symmetries. You have fine control each element
+ in the figure to tailor its focus points and detail to your audience.
+
+Package: circos-tutorials
+Architecture: any
+Depends: ${misc:Depends}
+Description: Contains tutorials
+ Usage and examples for Circos
Added: trunk/packages/circos/trunk/debian/copyright
===================================================================
--- trunk/packages/circos/trunk/debian/copyright (rev 0)
+++ trunk/packages/circos/trunk/debian/copyright 2011-06-30 11:32:37 UTC (rev 7187)
@@ -0,0 +1,42 @@
+Format: http://dep.debian.net/deps/dep5
+Upstream-Name: circos
+Source: http://circos.ca/
+
+Files: *
+Copyright: Copyright 2004-2011 Martin Krzywinski
+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 <http://www.gnu.org/licenses/>
+ .
+ On Debian systems, the complete text of the GNU General
+ Public License version 2 can be found in "/usr/share/common-licenses/GPL-2".
+
+Files: debian/*
+Copyright: 2011 Olivier Sallou <olivier.sallou at irisa.fr>
+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 <http://www.gnu.org/licenses/>
+ .
+ On Debian systems, the complete text of the GNU General
+ Public License version 2 can be found in "/usr/share/common-licenses/GPL-2".
+
Added: trunk/packages/circos/trunk/debian/docs
===================================================================
--- trunk/packages/circos/trunk/debian/docs (rev 0)
+++ trunk/packages/circos/trunk/debian/docs 2011-06-30 11:32:37 UTC (rev 7187)
@@ -0,0 +1 @@
+debian/README
Added: trunk/packages/circos/trunk/debian/patches/debianpackaging
===================================================================
--- trunk/packages/circos/trunk/debian/patches/debianpackaging (rev 0)
+++ trunk/packages/circos/trunk/debian/patches/debianpackaging 2011-06-30 11:32:37 UTC (rev 7187)
@@ -0,0 +1,8 @@
+--- a/bin/circos
++++ b/bin/circos
+@@ -1,4 +1,4 @@
+-#!/bin/env perl
++#!/usr/bin/env perl
+
+ =pod
+
Added: trunk/packages/circos/trunk/debian/patches/series
===================================================================
--- trunk/packages/circos/trunk/debian/patches/series (rev 0)
+++ trunk/packages/circos/trunk/debian/patches/series 2011-06-30 11:32:37 UTC (rev 7187)
@@ -0,0 +1 @@
+debianpackaging
Added: trunk/packages/circos/trunk/debian/rules
===================================================================
--- trunk/packages/circos/trunk/debian/rules (rev 0)
+++ trunk/packages/circos/trunk/debian/rules 2011-06-30 11:32:37 UTC (rev 7187)
@@ -0,0 +1,30 @@
+#!/usr/bin/make -f
+# -*- makefile -*-
+# Sample debian/rules that uses debhelper.
+# This file was originally written by Joey Hess and Craig Small.
+# As a special exception, when this file is copied by dh-make into a
+# dh-make output file, you may use that output file without restriction.
+# This special exception was added by Craig Small in version 0.37 of dh-make.
+
+# 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 svg/include \/usr\/share\/circos\/svg/g'
+ find debian/circos -type f | xargs sed -i 's/include tiles/include \/usr\/share\/circos\/tiles/g'
+ find debian/circos -type f | xargs sed -i 's/include data/include \/var\/lib\/circos\/data/g'
+ find debian/circos-tutorials -type f | xargs sed -i 's/include etc/include \/usr\/share\/circos\/etc/g'
+ find debian/circos-tutorials -type f | xargs sed -i 's/include fonts/include \/usr\/share\/circos\/fonts/g'
+ find debian/circos-tutorials -type f | xargs sed -i 's/include svg/include \/usr\/share\/circos\/svg/g'
+ find debian/circos-tutorials -type f | xargs sed -i 's/include tiles/include \/usr\/share\/circos\/tiles/g'
+ find debian/circos-tutorials -type f | xargs sed -i 's/include data/include \/var\/lib\/circos\/data/g'
+ find debian/circos-tutorials -type f | xargs sed -i 's/= data/= \/var\/lib\/circos\/data/g'
+
Property changes on: trunk/packages/circos/trunk/debian/rules
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/packages/circos/trunk/debian/source/format
===================================================================
--- trunk/packages/circos/trunk/debian/source/format (rev 0)
+++ trunk/packages/circos/trunk/debian/source/format 2011-06-30 11:32:37 UTC (rev 7187)
@@ -0,0 +1 @@
+3.0 (quilt)
Added: trunk/packages/circos/trunk/debian/watch
===================================================================
--- trunk/packages/circos/trunk/debian/watch (rev 0)
+++ trunk/packages/circos/trunk/debian/watch 2011-06-30 11:32:37 UTC (rev 7187)
@@ -0,0 +1,2 @@
+verison=3
+http://circos.ca/distribution/circos-(.*).tar.gz
More information about the debian-med-commit
mailing list