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Circos Builder (Galaxy Version 0.9-RC2) tool issue - pending fix, then update main to latest in MTS #105

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jennaj opened this issue Mar 21, 2018 · 7 comments
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Circos Builder (Galaxy Version 0.9-RC2) tool issue - pending fix, then update main to latest in MTS #105

jennaj opened this issue Mar 21, 2018 · 7 comments
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bug install usegalaxy.org tool install usegalaxy.org requested

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@jennaj
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jennaj commented Mar 21, 2018 •
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These errors look like dependency problems. Could we check?

Tool ID | toolshed.g2.bx.psu.edu/repos/iuc/circos/circgraph/0.9-RC2
Tool Version | 0.9-RC2

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

Examples, I could be using it wrong, but it looks like if anything other than the baseline karyotype input is added in, the tool fails.

dataset 15

screen shot 2018-03-21 at 10 42 50 am

screen shot 2018-03-21 at 10 43 07 am

dataset 22

screen shot 2018-03-21 at 10 41 42 am

Mismatched inputs are also a problem and could be handled better, but that issue is for the tool developers to address:

dataset 9

screen shot 2018-03-21 at 10 51 45 am

@natefoo @davebx
@jennaj jennaj added the bug label Mar 21, 2018
@jennaj jennaj mentioned this issue Mar 21, 2018
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@hexylena
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hexylena commented Mar 23, 2018 •
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I'll look into these over the next week. (Just fyi @shiltemann). These are probably all problems on the galaxy tool end :/

  • dataset 15 probably something wrong with my automatic processing of the files, maybe something has resulted in a 0 score somewhere and then this is being used in circos math somewhere. If it's a bug on our end maybe we can guard against it.
  • dataset 22 ur I'm guessing is coming from purples and something is going wrong there.
  • dataset 9 this is just a tool bug (the XML is so bloody complex, it is easy to miss this stuff, sorry it happened :( )

@hexylena
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(Alternate explanation: this is why it's RC2? Now maybe we'll get a 1.0 out of it that there's more real-world testing.)

@jennaj jennaj mentioned this issue Mar 26, 2018
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@jennaj jennaj added the install usegalaxy.org tool install usegalaxy.org requested label May 16, 2018
@jennaj
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jennaj commented May 16, 2018 •
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Retesting.

The HISAT2 link in a cross-tool problem related to this in behavior (same error reported), used as an example in the discussion. Ignore it unless very interested :) A HISAT2 update has been requested in another playbook ticket.

@jennaj jennaj added the test/retest-do active tests label May 16, 2018
@martenson martenson removed the install usegalaxy.org tool install usegalaxy.org requested label May 21, 2018
@jennaj jennaj added the functionality usegalaxy.org tool/dependency/function fix usegalaxy.org label May 21, 2018
@jennaj jennaj added test/retest-fail failed retest and removed test/retest-do active tests labels Jun 4, 2018
@jennaj
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jennaj commented Jun 4, 2018

Failed retest, still needs a fix

@jennaj jennaj mentioned this issue Jun 4, 2018
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@jennaj jennaj changed the title Circos Builder (Galaxy Version 0.9-RC2) dependency issues? Circos Builder (Galaxy Version 0.9-RC2) tool issue - pending fix, then update main to latest in MTS Jun 4, 2018
@jennaj jennaj added install usegalaxy.org tool install usegalaxy.org requested and removed functionality usegalaxy.org tool/dependency/function fix usegalaxy.org labels Jun 4, 2018
@jennaj jennaj mentioned this issue Jun 4, 2018
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@jennaj
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jennaj commented Jun 4, 2018

Created ticket at IUC repo since it is tool bug. This ticket is now for tracking that fix back to .org (once done).

galaxyproject/tools-iuc#1919

@hexylena
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hexylena commented Jun 5, 2018

Yeah, we still haven't patched it, I'm awful sorry. it's been a busy month unfortunately. The usegalaxy.eu server is feeling a bit more stable for the moment so maybe I can find time to do it.

@bellenger-l bellenger-l mentioned this issue Oct 4, 2018
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@jennaj
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jennaj commented Nov 1, 2021

This version was resolved a while ago. Closing

@jennaj jennaj closed this as completed Nov 1, 2021
@jennaj jennaj removed the test/retest-fail failed retest label Nov 1, 2021
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