[med-svn] r7436 - trunk/packages/circos/trunk/debian

Sat Aug 13 13:40:56 UTC 2011

Author: plessy
Date: 2011-08-13 13:40:55 +0000 (Sat, 13 Aug 2011)
New Revision: 7436

Removed:
   trunk/packages/circos/trunk/debian/README
Modified:
   trunk/packages/circos/trunk/debian/docs
Log:
Use upstream's README.


Deleted: trunk/packages/circos/trunk/debian/README
===================================================================

--- trunk/packages/circos/trunk/debian/README	2011-08-13 03:08:12 UTC (rev 7435)
+++ trunk/packages/circos/trunk/debian/README	2011-08-13 13:40:55 UTC (rev 7436)
@@ -1,152 +0,0 @@
-
-                                   / ___(_)_ __ ___ ___  __
-                                  | |   | | '__/ __/ _ \/ __|
-                                  | |___| | | | (_| (_) \__ \
-                                   \____|_|_|  \___\___/|___/
-
-                                                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/.
-
-If you are using Circos, please cite us: Krzywinski, M. et al. Circos: an Information Aesthetic for Comparative Genomics. Genome Res (2009) 19:1639-1645
-
-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/

Modified: trunk/packages/circos/trunk/debian/docs
===================================================================
--- trunk/packages/circos/trunk/debian/docs	2011-08-13 03:08:12 UTC (rev 7435)
+++ trunk/packages/circos/trunk/debian/docs	2011-08-13 13:40:55 UTC (rev 7436)
@@ -1,4 +1,4 @@
-debian/README
+README
 CHANGES
 README.tools
 README.tutorials


