Update Circos tool suite at usegalaxy.org
jennaj opened this issue · comments
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+galaxy80.69.8+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 version0.69.8+galaxy7works 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 for0.69.8+galaxy8and0.69.8+galaxy7are 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+galaxy10should resolve all known issues. See tool repo history here: https://github.com/galaxyproject/tools-iuc/commits/master/tools/circos
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)
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
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 :)
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.
Didn't actually install. Not sure why.
Oh, unmerged commits -- galaxyproject/usegalaxy-tools#482
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.
Great, thank you!
I'm going to close out the open tickets -- the tool runs whoohoo