CIRCOS fatal error

I am using Circos visualizes data in a circular layout (Galaxy Version 0.69.8+galaxy4) and it is giving fatal error since the 15th, after your maintenance.

I am using usegalaxy.org

Use of uninitialized value in subroutine entry at /cvmfs/main.galaxyproject.org/deps/_conda/envs/mulled-v1-dd38f3b35796eaa94d0b5d1d9c1428ec987dcd7f39e81a08df8df138203a8004/bin/…/lib/Circos/Configuration.pm line 781.
Can’t call method “colorExact” on an undefined value at /cvmfs/main.galaxyproject.org/deps/_conda/envs/mulled-v1-dd38f3b35796eaa94d0b5d1d9c1428ec987dcd7f39e81a08df8df138203a8004/bin/…/lib/Circos/Colors.pm line 348, line 6.

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Hi @jaiswalp, I’m one of the tool authors.

The earlier versions of the wrapper had some significant bugs in the color functions, those should all be fixed in the newer version. Please try 0.69.8+galaxy7 if it is available on .org.

It should be available on UseGalaxy.eu.

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Thanks @hxr! Agree – use the upgraded tools at usegalaxy.eu for at least the near-term.

@jaiswalp Upgrading the tool at usegalaxy.org will likely occur soon, but not immediately. Tracking ticket here https://github.com/galaxyproject/usegalaxy-playbook/issues/313. You and anyone else can follow it for updates.

Best

Thank you.
Pankaj

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Hello @hxr , I got quite a similar error like this topic when I followed the tutorial Visualisation with Circos (galaxyproject.org). The Circos version installed on our institution Galaxy is 0.69.8+galaxy7.

 Can't call method "colorExact" on an undefined value at /services/galaxy/galaxy_share/tool_deps/_conda/envs/mulled-v1-3cf5c7d734898be0f8d76d0fbf3face5f99ca4b3a9b294235f9271dd27115368/bin/../lib/Circos/Colors.pm line 348, <F> line 886.

Any ideas to fix it?

Many thanks
Thanh

ping @hxr for tool installation/config help

@thanhleviet To help troubleshoot. would you please write back and note:

  1. The version of Galaxy you are running?
  2. Has it been recently updated to capture any intermediate point updates since first installed?
  3. Upgrading to the latest release may help, so please give that a try. Consider saving a backup of what is running now in case you need to restore to that. If there are reasons an update is not possible, please explain.
  4. *Releases — Galaxy Project 21.01 documentation

Hi @jennaj

Thanks for your response, I guess it could be due to galaxy version? I’m using a bit old one 19.05, will try to upgrade to the latest one.

Best,
Thanh

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Hi @thanhleviet, I need a bit more information. Can you share the entire error message / stderr / stdout of the tool? Sometimes the error is hiding under the circos errors. Usually that happens when incorrectly formatted/not enough data is provided to Circos.

Can you share your datasets and parameters as well? That would significantly help with debugging if it’s possible that it can be shared?

Edit: I see you said you’re following the GTN tutorial. This absolutely should work, which portion were you following? The Cancer example is the most well tested, but perhaps you were doing one of the other plots?

If you were following the cancer one, which step did it fail at? If you can still share the screenshots/stderr/stdout of the failing job it would be helpful!

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