Note: In windows, there is no cat command, use 'more' instead. Pipe operator still applies in windows.
A modified tutorial for Windows 7/Vista; first you need to call up strawberry perl terminal and navigate to tableviewer directory
first, create a 3x3 table (use a random seed so that this step is reproducible)
> perl bin\make-table -row 3 -seed 123 -brief > samples\table-basic.txt
# let's see the table
> more samples\table-basic.txt
lbl A B C
A 262 209 168
B 28 86 45
C 58 95 69
# now parse the table
> more samples\table-basic.txt | bin\parse-table > tmp.txt
# now create configuration and data files
> more tmp.txt | bin\make-conf -dir data
# let's see what was created
> dir data/
Directory of c:\circos-0.55\tools\tableviewer\data
01/24/2012 10:35 PM <DIR> .
01/24/2012 10:35 PM <DIR> ..
01/24/2012 10:35 PM 255 all.txt
01/24/2012 10:35 PM 261 cap.col.txt
01/24/2012 10:35 PM 247 cap.row.txt
01/24/2012 10:35 PM 740 cells.txt
01/24/2012 10:35 PM 255 col.txt
01/24/2012 10:35 PM 62 colors.conf
01/24/2012 10:35 PM 598 colors_percentile.conf
01/24/2012 10:35 PM 72 karyotype.txt
01/24/2012 10:35 PM 249 row.txt
01/24/2012 10:35 PM 48 scaling.conf
01/24/2012 10:35 PM 33 segmentlabel.txt
11 File(s) 2,820 bytes
2 Dir(s) 20,571,529,216 bytes free
# now draw the image (circos.conf is already defined to use the data files from data/) (suppose you are still in 'tableviewer' directory
> perl ..\..\bin\circos -conf etc/circos.conf -outputfile table-basic.png
3 comments:
I'm having trouble with this step:
> more samples\table-basic.txt | bin\parse-table > tmp.txt
First of all, the command line doesn't understand bin\parse-table. I assume you meant to include "perl" there.
When I add "perl" I get many occurrences of this error:
Use of uninitialized value within @_ in lc at C:/strawberry/perl/site/lib/Graphics/ColorObject.pm line 1905, lin
e 5.
The tmp.txt file is still generated. Does this error matter?
If I proceed with making the conf file, I get this error when calling Circos:
*** CIRCOS ERROR ***
CONFIGURATION FILE ERROR
You did not include the etc/housekeeping.conf file in your configuration file.
This file contains many important system parameters and must be included in
each Circos configuration.
To do so, use
<>
in your main configuration file. For an example, see
http://www.circos.ca/documentation/tutorials/quick_guide/hello_world/configuration
If you have made other provisions to include these parameters, make sure you
have
housekeeping = yes
defined to skip this check.
If you are having trouble debugging this error, use this tutorial to learn how
to use the debugging facility
http://www.circos.ca/tutorials/lessons/configuration/debugging
If you're still stumped, get support in the Circos Google Group
http://groups.google.com/group/circos-data-visualization
Stack trace:
at D:/Users/Jordan/Documents/Programming/CIRCOS/circos-0.63-pre11/bin/../lib/Circos/Error.pm line 337.
Circos::Error::fatal_error('configuration', 'no_housekeeping') called at D:/Users/Jordan/Documents/Programming/C
IRCOS/circos-0.63-pre11/bin/../lib/Circos/Configuration.pm line 303
Circos::Configuration::populateconfiguration('configfile', 'etc\circos.conf', 'outputfile', 'table-jordan.png')
called at D:/Users/Jordan/Documents/Programming/CIRCOS/circos-0.63-pre11/bin/../lib/Circos.pm line 176
Circos::run('Circos', 'outputfile', 'table-jordan.png', 'configfile', 'etc\circos.conf') called at ..\..\..\circ
os-0.63-pre11\bin\circos line 299
Any suggestions?
@halfawake I think the issue in your first comment is no problem. For the second comment you need to replace the circos.conf file in the download with an updated one (that includes the housekeeping.conf file) which I got here...
https://groups.google.com/forum/?fromgroups=#!topic/circos-data-visualization/UKooW5yqdM8
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