Update Circos tool suite at usegalaxy.org

[jennaj]

Workaround for End-Users:

Please try the latest version of the tool at usegalaxy.eu: Circos visualizes data in a circular layout (Galaxy Version 0.69.8+galaxy8 0.69.8+galaxy10). Avoid earlier versions if using "Circos Presets" for Karyotype.

Problem reported/confirmed 10/27/21 Galaxy Help post: https://help.galaxyproject.org/t/circos-functional-on-usegalaxy-eu-but-not-usegalaxy-org/6972

Test histories (GTN test data)

• https://usegalaxy.org/u/jen-galaxyproject/h/test-circos
• https://usegalaxy.eu/u/jenj/h/test-circos

cc @davebx

MTS: https://toolshed.g2.bx.psu.edu/view/iuc/circos/7f13dc906cb9

More context

• The prior version 0.69.8+galaxy7 works fine at EU but not at ORG, so there is probably more going on than just the need to update to the latest wrapper. Maybe the dependencies for 0.69.8+galaxy8 and 0.69.8+galaxy7 are the same (?) and updating to the latest runtime container environment will address both. Perhaps @hexylena has some insight around that.
• Upgrading to 0.69.8+galaxy10 should resolve all known issues. See tool repo history here: https://github.com/galaxyproject/tools-iuc/commits/master/tools/circos

[jennaj]

Current version is now: 0.69.8+galaxy10

MTS: https://toolshed.g2.bx.psu.edu/view/iuc/circos/290a11559985

Note: Includes at least one other distinct bug fix ("Chrom presets" wasn't functional anywhere, any version version 0.69.8+galaxy7 or later)

[jennaj]

Fails tests: https://github.com/mvdbeek/usegalaxy-tests/issues/26

@bgruening @hexylena -- what version of the tool should we update to?

Also asked here: https://matrix.to/#/!RbhnsnsUHtkKuXuMDM:gitter.im/$XW7_xwK1nnUKLIjTKVLwBfdHY3qjii8A35bPkHDtZVI?via=gitter.im&via=matrix.org

.org is at 0.69.8+galaxy7 (known issue re karyotype index, but doesn't impact GTN tutorial afaik) .eu is at 0.69.8+galaxy9 mts is at 0.69.8+galaxy10

cc @davebx

[hexylena]

please update to galaxy10 @jennaj

For circos you can always just wait for my answer, I promise I'll answer whenever I'm awake. I'm still maintaining that tool and can offer the best commentary about which version :)

[jennaj]

Thank you and apologies for posting in the matrix chat about the same question!!

We can try get this updated before Monday if possible. If more delays, I think we should add to the visualisation_circos's tutorial channel in the pinned FAQ to run at eu or au instead.

[jennaj]

Didn't actually install. Not sure why.

Oh, unmerged commits -- https://github.com/galaxyproject/usegalaxy-tools/pull/482

[jennaj]

Not sure what we need to do. Can you help @hexylena?

The version sorting isn't working correctly when loaded from the tool panel (defaults to the 7 version, not the new 10 version). And the tool is failing for what looks like the original karyotype issue.

https://usegalaxy.org/u/jen/h/test-history-circos

[dannon]

@jennaj The tool version sorting is being looked into by @natefoo; he has some work in progress that will resolve this.

[jennaj]

Great, thank you!

I'm going to close out the open tickets -- the tool runs whoohoo

[hexylena]

@jennaj do you have a still failing circos history, I think I've recently seen one potential cause of the specific failure and I want to check.