configuration file error

[himani malhotra]

I have tried giving absolute and relative path,but each time i am getting this error of configuration file.


*** CIRCOS ERROR ***

      cwd: /home/i/Desktop/circus/data_test_CIRCUS_2.7

      command: /usr/bin/circos -conf tmp_dir/circos.conf

  CONFIGURATION FILE ERROR

  Error parsing the configuration file. You used an <<include FILE>> directive,
  but the FILE could not be found. This FILE is interpreted relative to the
  configuration file in which the <<include>> directive is used. Circos lookd
  for the file in these directories

  /etc/circos

  tmp_dir

  tmp_dir/etc

  /usr/bin/etc

  /usr/bin/../etc

  /usr/bin/..

  /usr/bin

  The Config::General module reported the error

  Config::General The file "etc/colors_fonts_patterns.conf" does not exist
  within ConfigPath:
  /etc/circos.tmp_dir.tmp_dir/etc./usr/bin/etc./usr/bin/../etc./usr/bin/.../usr/bin!
  at /usr/share/perl5/Circos/Configuration.pm line 820.

  If you are having trouble debugging this error, first read the best practices
  tutorial for helpful tips that address many common problems

      http://www.circos.ca/documentation/tutorials/reference/best_practices

  The debugging facility is helpful to figure out what's happening under the
  hood

      http://www.circos.ca/documentation/tutorials/configuration/debugging

  If you're still stumped, get support in the Circos Google Group. Please
  include this error and all your configuration and data files.

      http://groups.google.com/group/circos-data-visualization

  Stack trace:
 at /usr/share/perl5/Circos/Error.pm line 423.
    Circos::Error::fatal_error("configuration", "cannot_find_include", "/etc/circos\x{a}tmp_dir\x{a}tmp_dir/etc\x{a}/usr/bin/etc\x{a}/usr/bin/../etc\x{a}"..., "Config::General The file \"etc/colors_fonts_patterns.conf\" doe"...) called at /usr/share/perl5/Circos/Configuration.pm line 826
    Circos::Configuration::loadconfiguration("tmp_dir/circos.conf") called at /usr/share/perl5/Circos.pm line 143
    Circos::run("Circos", "configfile", "tmp_dir/circos.conf", "_argv", "-conf tmp_dir/circos.conf", "_cwd", "/home/i/Desktop/circus/data_test_CIRCUS_2.7") called at /usr/bin/circos line 385
Please help me out if there is any solution.
Thank you
Himani

[Martin Krzywinski]

This is happening because you've moved the circos binary into /usr/bin and the script cannot find files bundled with the distribution, because now these files are no longer in the expected relative directory positions.

The right way to install Circos is to unpack it somewhere, e.g.

/opt/circos-0.69

then link to 

/usr/bin/circos -> /opt/circos-0.69/bin/circos

m

Martin Krzywinski

science + art

http://mkweb.bcgsc.ca

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