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 - [email protected] -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 _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
