Re: [circos] Example tutorial from 0.62 (potential issues)

[Martin Krzywinski]

Hi Tom,

The example is meant to be self-contained - all the files it needs are within the example/ directory. The karyotype and data files are in example/data - that's where you'll find the *.bundle.txt files.

These files used to be within the Circos data/ directory, but now that the tutorials, which contain the data/ directory, are distributed as a separate archive, it felt more modular to have an example that is entirely independent.

But now that I think about it, duplicating the karyotype files seems pointless. I cannot think of a situation in which the ones that are included in the Circos distribution (data/karyotype) would be missing - except in the case where the user deletes the data/ directory. 

For the next version, the example karyotype.and.layout.conf file will pull these files from the Circos distribution, rather than example/data:

karyotype = data/karyotype/karyotype.human.txt,data/karyotype/karyotype.mouse.txt,data/karyotype/karyotype.rat.txt

In the past, I had Circos up on Google code, but nobody used it and it was more work for me to maintain the repository.

This might be a good time to try again with github :) I'm ready to be convinced!

Martin Krzywinski

science + art

http://mkweb.bcgsc.ca

On Mon, Jul 2, 2012 at 10:14 PM, Tom Schenk Jr <tomsc...@gmail.com> wrote:

Hi Martin-

I think I found a few issues. In the Circos example under example/etc/ the file karyotype.and.layout.conf points to "data/karyotype.human.txt" and a few other karyotype files under the data/ folder. However, the proper directory should be data/karyotype/karyotype.human.txt and the other files should also be under the data/karyotype directory (or, to reorganized the directory to just data/file).

Also, I don't see the files rn.bundle.txt, mm.bundle.txt, and several files which are suppose to be under the data/ directory, according to the circos.conf file. I haven't pulled up prior versions--laziness on my part--to see if these were just lost in the recent version(s).

As an aside, have you thought about hosting Circos on github so we can suggest modifications through their pull system?

Warm regards.

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[Tom Schenk Jr]

Hrm, ok, that makes sense, but I think the data/ folder was left-out of /example/ by mistake. The *.bundle.txt files aren't anywhere in the 0.62 release, but I did check 0.61 and found them under example/exampledata/. It looks like that folder didn't get tarball'd in the most recent release.

I think github is great--I never got into SourceForge or Google Code in the same way. Github seems to have a larger network of contributors with really easy commit/pulls/changes (through the terminal or a GUI). Like this issue, it would probably have been quicker for you to just look at my pull request and commit those changes (e.g., I could have just uploaded the missing files) without much work on your end.

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[Martin Krzywinski]

Oops, you're right - example/data is missing from 0.62.

I renamed example/exampledata to example/data to be more consistent. I think my packaging script erroneously left it out of the tarball.

I'll put up 0.62-1 now to fix this.

I haven't used github yet. I'll look into it.

Martin Krzywinski

science + art

http://mkweb.bcgsc.ca

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[Tom Schenk Jr]

Ah, makes plenty of sense. Well-meaning, logical changes never go unpunished...

One more question, then. The example is being executed from example/etc/circos.conf, which contains links to--for example--data/heatmap.hs.mm.20e6.txt (the karyotype data works just fine). But given the folder structure, Circos does not look at example/data/karyotype.human.txt. Instead, it's looking in bin, bin/etc, bin/data, ~/etc, ~/data, data--pretty much everywhere else except example/data/. Should the data in example/data/ be placed in the data/ folder in the Circos root directory?

P.S. A relevant side note, I'm trying to do this in Windows. I usually do it in Linux (thus, running the example), so I'm not sure if I'm running into some OS-specific stickiness.

Thanks!

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[Martin Krzywinski]

When asked for a file that has a relative path (e.g. data/heatmap.hs.mm.20e6.txt) circos will iterate through the following loops to find the file

for d1 in CWD,CIRCOSDIR

 for d2 in . .. ../.. ../.././.

  for d3 in . etc data

   look_for_file(d1/d2/d3/FILE)

where

  CWD - current directory

  CIRCOSDIR - circos directory

  FILE - requested file

If you run the example from the 'example/' directory, e.g.

> cd example

> circos

then when it comes to the data/heatmap.hs.mm.20e6.txt file, Circos will look in data/ within example/.

To see that this is happening, turn on the 'io' debugging.

> circos -debug_group io

...

debuggroup io 9.82s locating file data/heatmap.hs.mm.20e6.txt role heatmap track id track_3

debuggroup io 9.82s trying /home/martink/work/circos/svn/example/data/heatmap.hs.mm.20e6.txt

debuggroup io 9.82s data/heatmap.hs.mm.20e6.txt found in /home/martink/work/circos/svn/example/data/heatmap.hs.mm.20e6.txt

debuggroup summary 9.82s reading data and processing heatmap track id track_3 from /home/martink/work/circos/svn/example/data/heatmap.hs.mm.20e6.txt

...

I hope this is working as intended under Windows. If the example runs, then it is, because there is no 

data/heatmap.hs.mm.20e6.txt

file under the Circos tree.

The reason why I don't want the data/ directory in the Circos root is that I would like to keep it bundled with the example. 

I hope this all makes sense...

Martin Krzywinski

science + art

http://mkweb.bcgsc.ca

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[Tom Schenk Jr]

Ah ha! Ok, now that makes sense. In Windows, one needs to execute from--at least--the example folder given the suggested syntax.

For instance, this does not work: C:\Users\myusername>perl "C:/Program Files (x86)/Circos/bin/circos" -conf example\etc\circos.conf -debug_group summary,timer

But this does work: C:\Program Files (x86)\Circos\example>perl "C:/Program Files (x86)/Circos/bin/circos" -conf example\etc\circos.conf -debug_group summary,timer

I don't recall that being an issue in Linux, but I was doing my own projects, not the example. Hope this helps someone else trying to get use to the Windows environment.

Thanks!

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[Martin Krzywinski]

Get the latest version - 0.63-pre11. There were a few releases in which the example was messed up.

Run the example from the example/ directory, not from example/etc. In other words, from the Circos directory

cd example/

./run

You'll see in the etc/circos.conf file that data file location is specified as data/FILENAME. When files are specified by their relative name, Circos attempts to guess the location of the file by looking relative to your current directory, or the Circos distribution directory. This search includes a few other combinations of paths (which will actually find the file if you run it from examples/etc), but you should not depend on it. 

For example, if I rename one of the data files in circos.conf to something that does not exist, Circos reports all the directories it scanned for the file

Cannot guess the location of file [data/xrn.bundle.txt]. Tried to look in the following directories

      /home/martink/work/circos/svn/example/.

      /home/martink/work/circos/svn/example/etc

      /home/martink/work/circos/svn/example/data

      /home/martink/work/circos/svn/example/../.

      /home/martink/work/circos/svn/example/../etc

      /home/martink/work/circos/svn/example/../data

      /home/martink/work/circos/svn/example/../../.

      /home/martink/work/circos/svn/example/../../etc

      /home/martink/work/circos/svn/example/../../data

      /home/martink/work/circos/svn/example/../../../.

      /home/martink/work/circos/svn/example/../../../etc

      /home/martink/work/circos/svn/example/../../../data

      /home/martink/work/circos/svn/bin/.

      /home/martink/work/circos/svn/bin/etc

      /home/martink/work/circos/svn/bin/data

      /home/martink/work/circos/svn/bin/../.

      /home/martink/work/circos/svn/bin/../etc

      /home/martink/work/circos/svn/bin/../data

      /home/martink/work/circos/svn/bin/../../.

      /home/martink/work/circos/svn/bin/../../etc

      /home/martink/work/circos/svn/bin/../../data

      /home/martink/work/circos/svn/bin/../../../.

      /home/martink/work/circos/svn/bin/../../../etc

      /home/martink/work/circos/svn/bin/../../../data

Martin Krzywinski

science + art

http://mkweb.bcgsc.ca

On Fri, Nov 23, 2012 at 5:33 AM, Jan Herbst <jash...@gmail.com> wrote:

Hi

1. Thank you for this very, very interesing application.
2. I got the 0.62.1 version, but it seems to me that there still is some problem with the data files. I tried to run the example from the tutorial and I got a message saying "Cannot guess the location of file [data/rn.bundle.txt].". I checked it and found the file in the .../example/data folder. But the program wasn't looking for it there - it was trying to find it in the core data folder and "around".
3. Now, as a newby to all that stuff, I ask myself what to do? Should I just copy the missing data from the example folder to the core data folder (rather not..)? Change the path in configuration file? Something else?

I would appreciate your advice on that. Apologize if my question is stupid - i'm just starting to dig into it. And I can't stop :)

Greetings
Jan

W dniu wtorek, 3 lipca 2012 21:46:21 UTC+2 użytkownik Martin napisał:

Oops, you're right - example/data is missing from 0.62.

I renamed example/exampledata to example/data to be more consistent. I think my packaging script erroneously left it out of the tarball.

I'll put up 0.62-1 now to fix this.

I haven't used github yet. I'll look into it.

Martin Krzywinski

science + art

http://mkweb.bcgsc.ca

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