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Perl 5.8.x, or newer, is highly recommended. In addition to the core
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modules that come with your Perl distribution, the following CPAN
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modules that come with your Perl distribution, some CPAN modules are required.
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On UNIX systems, for a list of modules required by Circos, run
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> ln -s /usr/bin/env env
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Now try creating an image from one of the tutorials.
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Now try creating the example image
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> bin/circos -conf tutorials/2/2/circos.conf
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If everything goes well, the program should terminate with a line
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created image at /tmp/circos-tutorial.png
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To get some verbose reporting, use
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> bin/circos -conf tutorials/2/2/circos.conf -debug
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Please see L<http://www.circos.ca> for documentation. There are a large number
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of tutorials that described how the configuration files are formatted.
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> ../bin/circos -conf etc/circos.conf
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To get some verbose reporting about file I/O , use
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> ../bin/circos -conf etc/circos.conf -debug_group io,summary
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Please see L<http://www.circos.ca> for documentation. There are a
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large number of tutorials that described how the configuration files
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are formatted. Tutorials need to be downloaded separately.
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There are several helper scripts located in tools/ that are designed
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There are several helper scripts, available separately, that are designed
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to aid you in processing your data.
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Many of these involve manipulating link files. These tools independent
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scripts and are covered in Tutorial 9.
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L<http://circos.ca/tutorials/lessons/utilities>
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http://circos.ca/tutorials/lessons/utilities
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The tools can be downloaded independently. Note that the stand-alone
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tools distribution may contain scripts that are newer than those
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GD does not draw rotated text correctly when the font size is
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small. For example, using a font size of 6pt, text drawn an an angle
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is drawn with letters upright. If you see this, increase the font size
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GD does not draw rotated text correctly when the font size is small
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for certain fonts. For example, using a font size of 6pt, text drawn
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an an angle is drawn with letters upright. If you see this, increase
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the font size of the text.
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Fonts with which this problem occurs are
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CMUTypewriter-Regular
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For this reason, TTF versions of these fonts are used, rather than OTF.
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3. INSTALLATION PROBLEMS
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3.a Missing modules
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http://www.circos.ca/documentation/tutorials/configuration/perl_and_modules/
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In order to run Circos you may need to install some modules from CPAN
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(www.cpan.org). You will need the modules listed at L<http://www.circos.ca/software/requirements>.
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4.b Typical errors and how to fix them
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4.b.1 Numerical parameter units
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Many numerical parameters in the .conf files require that you specify
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a unit. For a given parameter, one or more of these units may be required
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p - absolute size in pixels
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r - relative size, with the comparator being context sensitive
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e.g. relative tick size is relative to ideogram thickness
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e.g. relative tick label offset is relative to tick size
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u - chromosome units, as defined by chromosomes_unit
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b - bases, the natural unit along the ideogram
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n - no unit, explicitly stated
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If you receive an error message of the kind
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The parameter [ideogram/spacing/break_style/thickness] value [0.25] does not have
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the correct unit [saw n], which should be one of r,p at bin/circos line 3410
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main::unit_validate(0.25, 'ideogram/spacing/break_style/thickness', 'r', 'p') called atbin/circos line 3559
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main::draw_axis_break('HASH(0x8a81d10)') called at bin/circos line 872
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Then you have the wrong unit. Here the parameter at fault is
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ideogram/spacing/break_style/thickness
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It is defined to be 0.25 (no unit) but requires that it have a unit of
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either "r" (relative) or "p" (absolute).
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As Circos matures, and the configuration file syntax stabilizes, I am
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striving to standardize the requirement for units for all
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parameters. Previous versions were more tolerant and attempted to
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naively determine the unit automatically (e.g. if value was <1 then
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the unit was assumed relative) and you may find that after upgrading
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to a new version of Circos your old files are creating errors. Just
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add the units and you're good to go.
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4.b.1 Dealing with errors
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http://mkweb.bcgsc.ca/dev/circos/documentation/tutorials/configuration/errors/
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4.b.2 No text in figures
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http://search.cpan.org/dist/GD/
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This issue comes up a lot. Circos has this to say about it
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circos -fake font,ttf
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and many threads about it have been created on the message boards
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http://groups.google.com/group/circos-data-visualization/browse_thread/thread/c893b8b612c2c5cf
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2012 Feb 20 - added link to thread about TTF support and a command to fake TTF font error
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2012 Feb 5 - modified note on errors, added reference to external tutorials
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2011 Jul 25 - split Circos, tutorials and tools into separate archives
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2011 Jun 04 - started keeping track of history
added
removed
README
