Use the latest version of Circos and read Circos best practices—these list recent important changes and identify sources of common problems.
If you are having trouble, post your issue to the Circos Google Group and include all files and detailed error logs. Please do not email me directly unless it is urgent—you are much more likely to receive a timely reply from the group.
Don't know what question to ask? Read Points of View: Visualizing Biological Data by Bang Wong, myself and invited authors from the Points of View series.
1 — Configuration and Installation
7. Runtime Parameters
checking version
> circos -version circos | v 0.67-pre5 | 12 May 2014
checking for missing modules
> circos -modules ok 1.26 Carp ok 0.37 Clone ok 2.50 Config::General ok 3.33 Cwd ok 2.145 Data::Dumper ...
specifying the configuration file
All aspects of the image are controlled by the plain-text configuration file. I conventionally name this file circos.conf, but you can use whatever name you like.
This file is specified at run-time using the -conf flag an
> circos -conf myimage.conf
Using circos.conf is convenient because Circos will automatically attempt to find a file of this name for its configuration.
# automatically search for circos.conf
> circos
Circos will search each combination of the path A/B/C for the file where
A=cwd, location ofcircosscriptB=. .. ../.. ../../..C=. etc/ data/
For example, the following will be searched (among others)
./circos.conf ./etc/circos.conf ./../etc/circos.conf
To see a list of paths that are searched, use the -debug_group flag.
> circos -debug_group io
adjusting output image location
Use -outputdir and -outputfile to change the output image location and name. These parameters are typically set in the <image> block in the configuration file with the dir and file parameters
<image> dir = /path/to/your/output/directory file = yourimage.png ... </image>
but you can override them at the command-line
> bin/circos -conf etc/circos.conf
-outputdir /path/to/your/output/directory
-outputfile yourimage.png
dumping configuration values
To see all the internal configuration values, provide all parameters as you would normally to generate the image but also add -cdump. You'll see a formatted data structure of your image's configuration.
> circos ... -cdump
changing parameters on the command line
All configuration file parameters can be adjusted on the command line using the -param flag. The syntax is
circos -param block1/block2/.../name=value
which will change the parameter name in the block <block1><block2>, overriding any value already defined in the configuration file.
<block1> <block2> ... name
For example,
circos -param karyotype=myfile.txt ... circos -param image/radius=500p circos -param ideogram/show=no
You can undefine a parameter by changing its value to undef
circos -param chromosomes=undef
This will effectively remove the parameter from the configuration. There should be no reason to have to do this but it is included in cases where you want to avoid inheriting a parameter from the parent block in some cases.
The full list of shortcuts is
# check required modules modules # toggle options silent cdump debug help man version color_cache_rebuild color_cache_static # negatable toggle options (e.g. -png, -nopng) png svg warnings paranoid show_tick_labels show_ticks # options with arguments debug_group configfile outputdir outputfile # randomize all colors randomcolor
Use these as flags. For example,
circos -modules circos ... -nosvg circos ... -randomcolor