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Update Circos tool suite at usegalaxy.org #346

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jennaj opened this issue Nov 3, 2021 · 9 comments
Closed

Update Circos tool suite at usegalaxy.org #346

jennaj opened this issue Nov 3, 2021 · 9 comments
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functionality usegalaxy.org tool/dependency/function fix usegalaxy.org impacts tutorials training.galaxyproject.org install usegalaxy.org tool install usegalaxy.org requested

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@jennaj
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jennaj commented Nov 3, 2021

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)

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 jennaj added install usegalaxy.org tool install usegalaxy.org requested functionality usegalaxy.org tool/dependency/function fix usegalaxy.org impacts tutorials training.galaxyproject.org labels Nov 3, 2021
@jennaj
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jennaj commented Nov 30, 2021

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)
circos_Presets

@jennaj
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jennaj commented Mar 10, 2022

Fails tests: mvdbeek/usegalaxy-tests#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
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hexylena commented Mar 11, 2022

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
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jennaj commented Mar 11, 2022

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
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jennaj commented Mar 16, 2022

Didn't actually install. Not sure why.

Oh, unmerged commits -- galaxyproject/usegalaxy-tools#482

@jennaj jennaj reopened this Mar 16, 2022
@jennaj
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jennaj commented Mar 16, 2022

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
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dannon commented Mar 16, 2022

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

@jennaj
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jennaj commented Mar 16, 2022

Great, thank you!

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

@jennaj jennaj closed this as completed Mar 16, 2022
@hexylena
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@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.

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