Configuration file error (2 - different)

[Josie]

Hi guys, I am new to perl and circos and have gotten past Circos installation, module installation, etc., now just trying to run the circos script provided but keep getting the following (or related) error:

C:\circos\bin>perl C:\circos\bin\circos -conf circos.conf
debuggroup summary 0.23s welcome to circos v0.69-8 15 Jun 2019 on Perl 5.032001
debuggroup summary 0.23s current working directory C:/circos/bin
debuggroup summary 0.23s command C:\circos\bin\circos -conf circos.conf
debuggroup summary 0.23s loading configuration from file circos.conf

  *** CIRCOS ERROR ***

      cwd: C:/circos/bin

      command: C:\circos\bin\circos -conf circos.conf

  CONFIGURATION FILE ERROR

  Circos could not find the configuration file [circos.conf]. To run Circos, you
  need to specify this file using the -conf flag. The configuration file
  contains all the parameters that define the image, including input files,
  image size, formatting, etc.

  If you do not use the -conf flag, Circos will attempt to look for a file
  circos.conf in several reasonable places such as . etc/ ../etc

  To see where Circos looks for the file, use

      circos -debug_flag io

  To see how configuration files work, create the example image, whose
  configuration and data are found in example/. From the Circos distribution
  directory,

      cd example

      ../bin/circos -conf ./circos.conf

  or use the 'run' script (UNIX only).

  Configuration files are described here

      http://circos.ca/tutorials/lessons/configuration/configuration_files/

  and the use of command-line flags, such as -conf, is described here

      http://circos.ca/tutorials/lessons/configuration/runtime_parameters/

  Windows users unfamiliar with Perl should read

      http://circos.ca/tutorials/lessons/configuration/unix_vs_windows/

  This error can also be produced if supporting configuration files, such as
  track defaults, cannot be read.

  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 C:/circos/bin/lib/Circos/Error.pm line 425.
        Circos::Error::fatal_error("configuration", "missing", "circos.conf") called at C:/circos/bin/lib/Circos/Configuration.pm line 796
        Circos::Configuration::loadconfiguration("circos.conf") called at C:/Strawberry/perl/lib/Circos.pm line 148
        Circos::run("Circos", "_argv", "-conf circos.conf", "configfile", "circos.conf", "_cwd", "C:/circos/bin") called at C:\circos\bin\circos line 536 

Does it have to do with the back vs forward slash? I am running on Windows. Have tried replacing all '/' in the script to '\' to match with my command line. Any other ideas please??

Thanks in advance,

Desperate

[Josie]

I think I needed to add a .conf suffix to the circos text file that was in my circos\bin. Have done so, but now I'm stuck with the following error, where the path can't be found:

#this:

C:\>perl C:\circos\bin\circos -conf circos.conf

#now returns this:
Can't open perl script "C:\circos\bin\circos": No such file or directory

But, lies:

Any help appreciated! This will be a slow grind for me either way lol

Running circos | v 0.69-8 | 15 Jun 2019 | Perl 5.014002, for reference.

[Martin]

Your directory tree is a little wonky. You shouldn't have everything in bin/. 

Instead, unzip the distribution into C:\circos and you should get

C:\circos\circos-v0.69-9\

then

cd C:\circos\circos-v0.69-9\bin

perl circos

Don't move the location of files within the distribution tree. There's some internal logic that helps the script find files.

The circos.conf file will be automatically loaded from

bin\..\etc