configuration file error

[Nate]

Hey guys,

I followed the tutorial step by step but still get this error every time, any idea? 

Interestingly, the example works but nothing else. tried linking the environments and adding my "installation" folder to my PATH.

my_acc@server: ~/software/circos/circos-tutorials-0.67/tutorials/1/1$ circos -conf circos.conf

debuggroup summary 0.10s welcome to circos v0.69-8 15 Jun 2019 on Perl 5.030000
debuggroup summary 0.11s current working directory /home/narnold/software/circos/circos-tutorials-0.67/tutorials/1/1
debuggroup summary 0.11s command /bin/circos -conf circos.conf
debuggroup summary 0.11s loading configuration from file circos.conf
debuggroup summary 0.11s found conf file circos.conf

  *** CIRCOS ERROR ***

      cwd: /home/my_acc/software/circos/circos-tutorials-0.67/tutorials/1/1

      command: /bin/circos -conf 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

  .

  ./etc

  /usr/bin/etc

  /usr/bin/../etc

  /usr/bin/..

  /usr/bin

  The Config::General module reported the error

  Config::General The file "etc/image.conf" does not exist within ConfigPath:
  /etc/circos..../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.

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

  Please include this error, all your configuration, data files and the version
  of Circos you're running (circos -v). Do not email me directly -- please use
  the group.

  Stack trace:
 at /usr/share/perl5/Circos/Error.pm line 425.
    Circos::Error::fatal_error("configuration", "cannot_find_include", "/etc/circos\x{a}.\x{a}./etc\x{a}/usr/bin/etc\x{a}/usr/bin/../etc\x{a}/usr/bin/..\x{a}"..., "Config::General The file \"etc/image.conf\" does not exist with"...) called at /usr/share/perl5/Circos/Configuration.pm line 826
    Circos::Configuration::loadconfiguration("circos.conf") called at /usr/share/perl5/Circos.pm line 148

    Circos::run("Circos", "_cwd", "/home/narnold/software/circos/circos-tutorials-0.67/tutorials"..., "configfile", "circos.conf", "_argv", "-conf circos.conf") called at /bin/circos line 538

thanks,

Nate

[Martin]

It's not exactly clear what the problem is. But it definitely has something to do with files being in the wrong place.

The tutorials are meant to go in the circos directory. In other words, you want a structure like

circos-x.xx/

bin/circos

tutorials/

  1/  

    1/

  2/
  ...

> tried linking the environments and adding my "installation" folder to my PATH.

What do you mean by linking the environments?

Circos itself doesn't care about PATH. It's only useful for the shell to search for the script.

Also, did you at all separate the circos distribution files?

What's happening is that when Circos runs, it parses the config file and anytime it finds an <<include FILE>> it will look for FILE in a set of directories, which includes your current working directory and "etc/" relative to the cwd. If it doesn't find the file it looks to directories relative to the circos script. 

If you've separated the bin/ and etc/ directories in the distribution then Circos won't find the conf files.

<image>
# Included from Circos distribution.
<<include etc/image.conf>>
</image>

Circos is looking for etc/image.conf. This file is in etc/ in the distribution.

1. Where is the circos script?

2. Where is the etc/ directory from the distribution?

m

[Nate]

Hey Martin,

thank you for your swift reply!

I just meant the  ln -s /usr/bin/env env stuff in the installation guide, wasn't sure if that mattered (total unix noob here).

You were right & it works now! I didn't realize one had to:

 1) move the tutorial folder into circos/bin

2) as well as the tutorial/data into the circos/bin

3) in addition to the circos/etc into circos/bin

In hindsight looking at your example folder structure (which worked with the ./run script as it should) now it makes total sense.

Is there any particular reason not to put the circos/etc folder into the circos/bin folder right away, as safety measure to not screw things up or something?

Anyhow, thanks a ton and best regards,

Nate