Re: [circos] How to start Circos

[Martin Krzywinski]

You create configuration files using a text editor.

You then run the Circos binary and pass in the name of the file at the command line using the -conf flag.

If you're not familiar with using the command line, editing text files, or manipulating paths then check out some of the tutorials linked from

http://www.circos.ca/documentation/tutorials/configuration/unix_vs_windows/

The "karyotype ..." line you mention is one of the parameter definitions in the configuration file. It tells Circos where to look for its definition of chromosomes (size, name, color, etc). A configuration file contains a large number of such parameters to complete a working definition of how the image should look and what data should be used to create it.

There's a large number of tutorials that show different configuration files and build them up from scratch

http://www.circos.ca/documentation/tutorials/quick_start/

Most people use these as templates and change them as required to suit their project.

m

Martin Krzywinski

science + art

http://mkweb.bcgsc.ca

On Thu, Jan 19, 2017 at 8:25 AM, David van Reekum <d.van...@gmail.com> wrote:

Dear all,

I feel rather stupid not being able to actually generate a Circos diagram. I've read everything a couple of times but don't know how actually start. I've tried to find answers in the Googlegroup, but I think my problem is so minor that there isn't a topic for it. What am I missing here.

The Hello world tutorial starts with "karyotype = data/karyotype/karyotype.human.txt". Is this the configuration file? I get "command not found" when I try this command in the command prompt. Is there a specific cwd you need to be in before you can do this?

If you have your own data, you should specify a configuration file with the -conf flag command right? In what cwd should you be in before you use this command flag.

How can you specify a configuration file, how can you create/construct a configuration file, yourself and how should be able to you know if the specifying has worked? Can this be your own plain text file or should you always start with a given conf?

I hope someone can help!

Kind regards,

David

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[catherine laplace]

I have exactly the same issue as David, I have sucessfully installed all needed perl modules, I have read the tutorials a few times but it does not help me start ( I admit I am very new at this and the issue is probably so basic it does not occur to the teachers ). Sorry this answer did not help me at all.

 

Thank you in advance for any help to get me " unstuck"

Catherine

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[Wayne]

Hi Catherine, 

Are you able to generate the first image the tutorials start out with?  If not, I can at least get you to that point albeit not on your own computer. 

In your browser, go to https://github.com/fomightez/circos-binder and press the badge that says 'launch binder'. A an active Jupyter session will spin up. It already has Circos installed and working.

Click to `Getting Circos Up and Running` and it will step through running that very first demo that establishes things work.

You'll want to pay particular attention to what is described under 'Triggering the 'complex' example code to run'. That is showing how the first part of a command, i.e., the `../bin/circos` points at the location of the program binaries to call and then the second part, i.e.,  `-conf etc/circos.conf` points at the configuration files for circos to use.  You'd need to adjust the path when you are elsewhere. 

Unfortunately, while I intend to convert the other tutorial pages to be stepped through in working form similar to that first page (but with more of a Python slant), I haven't yet. And that would probably help you more. But in the hopes that having an environment where things work already helps a little, I am pointing this out.

Hope it helps,

Wayne

[catherine laplace]

Thank you Wayne, I was able to produce an image. my issue had something to do with the path.

Catherine

[nishat]

Does #!/bin env perl
Means circos running ?

[Wayne]

No. That is a shebang line that you would include at the top of a script to say to run it in perl. It is trying to generalize the path to perl to then run the script that follows with.

See https://www.cyberciti.biz/tips/finding-bash-perl-python-portably-using-env.html

[nishat]

okay then what command I need to type to run circos 

[Naman Mangukia]

Hi Nishat,

I am showing you the command for Linux OS.

The command requires mainly 2 types of elements:
<Path_to_the_circos_bin_executable> <config-file>

Example command:

/home/nishat/circos/bin/circos circos.config

Regards,

Naman

/

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[Wayne]

Hi Nishat,

There is a nice example where you can see what Neo says without needing to worry if you have installed everything.

Follow the directions I gave to Catherine above to see examples of what Neo says. I'll expand and update launching Circos for free on a remote machine in your browser here:

In your browser, go to https://github.com/fomightez/circos-binder and press the badge that says 'launch Circos on Jupyter'. And an active Jupyter session will spin up. It already has Circos installed and working. 

Click to `Getting Circos Up and Running` at the top of the first page that comes up and that notebook page will step through running that very first demo that establishes things work. (Don't dwell on understanding how circos is directed to work on this page too much because as I explain below I think it is more cryptic for novices because it runs an example that is streamlined to just work.)

The cells with brackets in front of them contain commands that will run on the command line when you run the cell. To run the cell, left-click in the cell with your mouse and then left-click on the `Run` button on the menu just above the notebook page. Alternatively, instead of left-clicking the `Run` button, you can type `SHIFT` and `ENTER` at the same time to run the selected cell.

The commands on that page  `Getting Circos Up and Running` will work as written even if see warning-like messages. (I just tested a launch myself and everything works.) But in fact it is very cryptic because it is running a pre-set example. However, knowing that works and tings are installed what is best to do is go try and test the stuff Neo says.

To test what Neo says you are better off going back to the first page that opened in your session and picking the page 'Quick Start: Part 1: Hello World' to open. Just be aware that notebook (and all others with the exception of the first one listed) adds in another layer because the code cells by default are directed to Python. (You'll see an indicator in the upper right corner of the notebook that is different than the `Getting Circos Up and Running` page has.)  You want to direct things to the bash command line  and not Python, and so you 'll see `%%bash` to direct commands in the cell running the circos command. (Somewhat confusingly for novices, the notebook cells are smart enough to recognize some bash commands and so you don't always need `%%bash` at the top of the cell for very basic, built-in unix commands. Running circos is NOT a built-in unix command, and so you need to direct that out to the bash shell.)