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For details about installation and use on Windows, please see
http://circos.ca/tutorials/lessons/configuration/unix_vs_windows/
http://circos.ca/tutorials/lessons/configuration/distribution_and_installation/
Specifically, be aware of the following:
1. Windows file paths use "\" as a directory separator, whereas UNIX
uses "/". The UNIX convention is used throughout the tutorials. Thus
when you see
tutorials/2/2/circos.conf
in any of the tutorials or documents, read
tutorials\2\2\circos.conf
2. From the command line, you'll need to run perl and use the circos script as the argument
perl bin\circos -conf tutorials\2\2\circos.conf
Windows won't know what to do with the bin\circos file otherwise.
3. By default, tutorial images are created in /tmp, a directory that
does not exist on Windows. You'll need to either (a) create this
directory or override the output directory by using the -outputdir
parameter
perl bin\circos -conf tutorials\2\2\circos.conf -outputdir c:\path\to\image\directory
You can change the output filename using -outputfile.
perl bin\circos [...] -outputfile myfile.png
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