Re: Circos: Command not found error in example file

[rohan]

Hello Prahlad,

I am having the same error as mentioned by you.

You must have been able to resolve it.Can you please let me know the issue here?

Thanks,

Rohan

On Wednesday, January 9, 2013 11:23:49 PM UTC-5, Prahlad Rao wrote:

Hello,
   I tried running this example that you have posted in http://www.circos.ca/presentations/articles/vis_tables2/:

# first, create a 3x3 table (use a random seed so that this step is reproducible)
> bin/make-table -row 3 -seed 123 -brief > samples/table-basic.txt
# let's see the table
> cat samples/table-basic.txt
 lbl    A    B    C
   A  262  209  168
   B   28   86   45
   C   58   95   69
# now parse the table
> cat samples/table-basic.txt | bin/parse-table > tmp.txt
# now create configuration and data files
> cat tmp.txt | bin/make-conf -dir data
# let's see what was created
> ls data/
-rw-r--r--  1 martink users 246 Jun  1 15:12 all.txt
-rw-r--r--  1 martink users 726 Jun  1 15:12 cells.txt
-rw-r--r--  1 martink users 246 Jun  1 15:12 col.txt
-rw-r--r--  1 martink users  52 Jun  1 15:12 colors.conf
-rw-r--r--  1 martink users 577 Jun  1 15:12 colors_percentile.conf
-rw-r--r--  1 martink users  69 Jun  1 15:12 karyotype.txt
-rw-r--r--  1 martink users 242 Jun  1 15:12 row.txt
# now draw the image (circos.conf is already defined to use the data files from data/)
> circos -conf etc/circos.conf -outputfile table-basic.png

I am able to make the random table, parse it and use the make-conf command but when I run the last line of the example, I get the error 
Prahlad-Raos-MacBook:tableviewer prao123$ ls data
all.txt			col.txt			row.txt
cap.col.txt		colors.conf		scaling.conf
cap.row.txt		colors_percentile.conf	segmentlabel.txt
cells.txt		karyotype.txt
Prahlad-Raos-MacBook:tableviewer prao123$ circos -conf etc/circos.conf -outputfile table_test.png
-bash: circos: command not found

I have tried the ./makeimage 01 command and that works but when I go through the example it fails at the last command. Could you point me in the right direction?

Thanks
Prahlad

[Martin Krzywinski]

You need to have circos in your PATH for that command to work.

Alternatively, reference the circos script explicitly. For example, if Circos is installed in /usr/local/circos then 

/usr/local/circos/bin/circos -conf ...

Martin Krzywinski

science + art

http://mkweb.bcgsc.ca

--
You received this message because you are subscribed to the Google Groups "Circos" group.

To unsubscribe from this group and stop receiving emails from it, send an email to circos-data-visual...@googlegroups.com.

To post to this group, send email to circos-data-...@googlegroups.com.

Visit this group at http://groups.google.com/group/circos-data-visualization.
For more options, visit https://groups.google.com/groups/opt_out.
 
 

[rohan]

Thanks a lot Martin.I am referrencing it separately and getting these errors:

Use of uninitialized value $key in split at /Applications/circos-0.63-4/bin/../lib/Circos/Debug.pm line 246.

Use of uninitialized value $key in split at /Applications/circos-0.63-4/bin/../lib/Circos/Debug.pm line 246.

  *** 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

      <<include etc/housekeeping.conf>>

  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 /Applications/circos-0.63-4/bin/../lib/Circos/Error.pm line 339

Circos::Error::fatal_error('configuration', 'no_housekeeping') called at /Applications/circos-0.63-4/bin/../lib/Circos/Configuration.pm line 304

Circos::Configuration::populateconfiguration('configfile', 'etc/circos.conf', 'outputfile', 'img/table-basic.png') called at /Applications/circos-0.63-4/bin/../lib/Circos.pm line 178

Circos::run('Circos', 'outputfile', 'img/table-basic.png', 'configfile', 'etc/circos.conf') called at /Applications/circos-0.63-4/bin/circos line 300

I have checked for 

      <<include etc/housekeeping.conf>>

in my circus.conf file and also for  housekeeping = yes.Both are present since I am using circos-0.63-4

To unsubscribe from this group and stop receiving emails from it, send an email to circos-data-visualization+unsub...@googlegroups.com.

[Martin Krzywinski]

Make sure that you're using the configuration file you think you are using!

When you use the relative path

-conf etc/circos.conf

Circos will use the configuration file in etc/ relative to your current directory. 

If you're running the command from a path that is far from where the configuration file is, it's best to use absolute path

-conf /path/to/circos.conf

Martin Krzywinski

science + art

http://mkweb.bcgsc.ca

To unsubscribe from this group and stop receiving emails from it, send an email to circos-data-visual...@googlegroups.com.

[rohan]

Hi Martin,

Do we have to write this "<<include etc/housekeeping.conf>>" in circos.conf file that is created ?

When I am including this it gives me error below:

Configuration parameter [warnings] in parent block [_root] has been defined

  more than once in the block shown above, and has been interpreted as a list.

  This is not allowed. Did you forget to comment out an old value of the

  parameter?

And when I am not including it, it asks me to include it

 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

      <<include etc/housekeeping.conf>>

  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.

I am giving this command with an absolute path for calling circos, which is present in Applications, and my current directory is table viewer

Rohans-MacBook-Pro:tableviewer rohan$ /Applications/circos-0.63-4/bin/circos -conf etc/circos.conf -outputfile table-basic.png

To unsubscribe from this group and stop receiving emails from it, send an email to circos-data-visualization+unsubsc...@googlegroups.com.

To post to this group, send email to circos-data-...@googlegroups.com.

Visit this group at http://groups.google.com/group/circos-data-visualization.
For more options, visit https://groups.google.com/groups/opt_out.
 
 

[rohan]

I am copying my circos.conf file below.I am not able to get which parameters is it taking twice:

# This is the main configuration file for the Circos tableviewer. This file also

# depends on colors.conf (definition on basic colors), ideogram.conf (size and spacing of

# row/cell segments), and ticks.conf (tick spacing and label definitions - these are turned

# off by default).

#

# In addition to these configuration files, the bin/make-conf script creates 

# colors.conf (colors of row/col segments) and colors_percentile.conf (colors based on

# cell percentile values). These configuration files are also included via the <<include>> directive.

#

# Some elements of the output image are toggled off by default (e.g. row and column highlights, 

# anchor links to segment labels, tick marks).

<colors>

<<include etc/colors.conf>>

<<include data/colors.conf>>

<<include data/colors_percentile.conf>>

</colors>

<fonts>

<<include etc/fonts.conf>>

</fonts>

<<include etc/ideogram.conf>>

<<include etc/ticks.conf>>

<<include circos-0.63-4/etc/housekeeping.conf>>

karyotype = data/karyotype.txt

<image>

dir   = img

file  = tableview.png

24bit = yes

svg   = yes

png   = yes

# radius of inscribed circle in image

radius         = 1500p

background     = white

# by default angle=0 is at 3 o'clock position

angle_offset   = -90

auto_alpha_colors = yes

auto_alpha_steps  = 5

</image>

chromosomes_units              = 10

chromosomes_display_default    = yes

chromosomes_order_by_karyotype = yes

<highlights>

show = yes

<highlight>

show = no

file = data/row.txt

r0 = 1r+200p

r1 = 1r+220p

stroke_color = black

stroke_thickness = 2

</highlight>

<highlight>

show = no

file = data/col.txt

r0 = 1r+230p

r1 = 1r+250p

stroke_color = black

stroke_thickness = 2

</highlight>

<highlight>

show = no

file = data/all.txt

r0 = 1r+10p

r1 = 1r+35p

stroke_color = black

stroke_thickness = 2

</highlight>

<highlight>

file = data/cap.col.txt

r0   = 0.999r-30p

r1   = 0.999r-10p

stroke_color = black

stroke_thickness = 1

</highlight>

<highlight>

file = data/cap.row.txt

r0   = 0.999r-20p

r1   = 0.999r

stroke_color = black

stroke_thickness = 1

</highlight>

</highlights>

<plots>

<plot>

type = text

file = data/segmentlabel.txt

label_font = condensedbold

color = black

label_size = 48p

r0   = 1r+100p

r1   = 1r+1000p

rpadding = 0p

padding = 0p

show_links     = no

link_dims      = 0p,10p,32p,10p,5p

link_thickness = 3p

link_color     = black

label_snuggle             = yes

# shift label up to its height in pixels in the angular direction

max_snuggle_distance      = 10r

snuggle_sampling          = 10

snuggle_tolerance         = 0.25r

</plot>

</plots>

<links>

<link cellvalues>

ribbon        = yes

flat          = yes

file          = data/cells.txt

bezier_radius = 0.0r

radius        = 0.999r-30p

thickness     = 1

color         = grey

stroke_color     = black

stroke_thickness = 1

<rules>

<rule>

importance = 95

condition  = 1

radius1    = 0.999r-20p

flow       = continue

</rule>

</rules>

</link>

</links>

anglestep       = 0.5

minslicestep    = 10

beziersamples   = 40

debug           = no

warnings        = no

imagemap        = no

units_ok = bupr

units_nounit = n

Thanks,

Rohan

[rohan]

Hi Martin,

I have been able to find the mistake.I have removed <<include etc/housekeeping.conf>> and added housekeeping =yes since I was getting this error:

Configuration parameter [warnings] in parent block [_root] has been defined

  more than once in the block shown above, and has been interpreted as a list.

  This is not allowed. Did you forget to comment out an old value of the

  parameter?

I am attaching the sample table and the figure which as created.Thanks a lot for assistance again.

Thanks,

Rohan

On Thursday, July 11, 2013 5:34:58 PM UTC-4, Martin wrote:

To unsubscribe from this group and stop receiving emails from it, send an email to circos-data-visualization+unsubsc...@googlegroups.com.

To post to this group, send email to circos-data-...@googlegroups.com.

Visit this group at http://groups.google.com/group/circos-data-visualization.
For more options, visit https://groups.google.com/groups/opt_out.
 
 

[Martin Krzywinski]

You need the housekeeping.conf file. It has a lot of required parameters.

However, you need to remove these lines from the configuration file. These parameters are already defined in housekeeping.conf, and an error is thrown when they are defined in duplicate.

### keep this

<<include etc/housekeeping.conf>>

### remove this

anglestep       = 0.5

minslicestep    = 10

beziersamples   = 40

debug           = no

warnings        = no

imagemap        = no

units_ok = bupr

units_nounit = n

### 

Martin Krzywinski

science + art

http://mkweb.bcgsc.ca

To unsubscribe from this group and stop receiving emails from it, send an email to circos-data-visual...@googlegroups.com.