circos custom config file unable to read default tracks

Bug #1547519 reported by Tamas Deak on 2016-02-19
14
This bug affects 2 people
Affects Status Importance Assigned to Milestone
circos (Ubuntu)
Undecided
Unassigned

Bug Description

Hi there,
If using a simple conf file for a circos image, ideograms are drawn, but if you're including any basic plots, you get an error message about circos not being able to read the configuration file.
This is caused by a relative path in /etc/circos/housekeeping.conf. If you change the line "track_defaults = etc/tracks" to "track_defaults = /etc/circos/tracks", everything is working like a charm.
Circos does not give a reasonable hint in debug mode and the problem is persistent since several months.

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Tamas Deak (deatomium) wrote :
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Ubuntu Foundations Team Bug Bot (crichton) wrote :

The attachment "housekeeping.conf.patch" seems to be a patch. If it isn't, please remove the "patch" flag from the attachment, remove the "patch" tag, and if you are a member of the ~ubuntu-reviewers, unsubscribe the team.

[This is an automated message performed by a Launchpad user owned by ~brian-murray, for any issues please contact him.]

tags: added: patch
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Launchpad Janitor (janitor) wrote :

Status changed to 'Confirmed' because the bug affects multiple users.

Changed in circos (Ubuntu):
status: New → Confirmed
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Kristian Loewe (loewe) wrote :

A workaround is to create a symlink (named etc) to /etc/circos in the directory that contains the configuration files for a given circos plot. This makes the suggested patch unnecessary. It additionally preserves the ability to use relative includes for other circos configuration files.

In my opinion, the best solution would be to add /etc/circos to circos' search path, though.
See also: http://circos.ca/tutorials/lessons/configuration/configuration_files/

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Tamas Deak (deatomium) wrote :

Thanks for the workaround Kristian, it works like a charm :)

This question is more "philosophical" than technical for me: I like the idea of using circos with fixed location for the config files. This way I can work in clean circos projects, where only project-specific files are located and no general config files (or symlinks to /etc/).

I agree that adding /etc/circos to the search path would be an ideal solution, but this is behind my capabilities. Actually, isn't line 801 of /usr/share/perl5/Circos/Configuration.pm meant to provide this functionality?

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