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galaxyproject / tools-iuc

Tool Shed repositories maintained by the Intergalactic Utilities Commission
https://galaxyproject.org/iuc
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HISAT2 2.1.0 fails when options under "Scoring options" used #1792

Closed jennaj closed 6 years ago

jennaj commented 6 years ago

Tool version 2.1.0 (most current): https://toolshed.g2.bx.psu.edu/view/iuc/hisat2/40e1083a4430

Test history: https://usegalaxy.org/u/jen/h/test-history-hisat2-soft-clip

I'll also test at https://usegalaxy.eu to make sure this isn't server-specific. The error does not look like a dependency problem, but a tool wrapper problem:

screen shot 2018-03-26 at 11 32 21 am
jennaj commented 6 years ago

Same results at Galaxy Europe https://usegalaxy.eu/u/jenj/h/test-history-hisat2-soft-clip-eu-server

mvdbeek commented 6 years ago

Yeah, all of https://github.com/galaxyproject/tools-iuc/blob/master/tools/hisat2/hisat2.xml#L231 need to be scoring_options.advanced.* instead of scoring_options.*

jennaj commented 6 years ago

Reported at https://biostar.usegalaxy.org/p/27285. If I can get around this with an earlier tool version, we can use that as a workaround until 2.1.0 is upgraded/fixed.

mvdbeek commented 6 years ago

nah, we can fix it quickly, just running the tests now

mvdbeek commented 6 years ago

BTW, all of these NotFound: cannot find 'xxxx' are definitely, 100% bugs all of the time -- if you have a means to systematically look at error reports and filter out failed runs for tools (latest version) I think that would be super helpful.

jennaj commented 6 years ago

Thank you! Very good to know. I wasn't sure if some errors with this message were server-dependancy problems or not - same error used to point to those (older tool versions, now that I reviewed them). Usage issues previously could also trigger the same message. I'll retest one like that (usage/input problem) in the new tool version using the problematic inputs and see what happens. Sure would simplify troubleshooting if these messages are now restricted to wrapper bugs.

Btw- All bugs reported from usegalaxy.org, with this error message, using newer tool versions, have tickets already and are confirmed tool bugs. Example: Circos Builder -- I should have put this in IUC repo, but comments already exist about it being a tool problem and it is being addressed, so think I'll leave it there -- unless you think I should move it? https://github.com/galaxyproject/usegalaxy-playbook/issues/105

Going forward, I'll report errors with this message directly to the tool dev repo and skip the vetting to eliminate a server-side issue first. (when bugs are reported is for the newer tool versions)

mvdbeek commented 6 years ago

This exact error only happens when a tool parameter is being referenced in the command section that is not (or not correctly) declared in the input / configfile or output section of the tool wrapper. You may need to select a very specific combination of parameters to get there, but if you do it is not a usage problem. Those corner cases sometimes slip through even with our reviews. This error message is not to be confused with command not found errors though, that does indeed indicate dependency problems.

jennaj commented 6 years ago

Hi @mvdbeek @bgruening - would it be OK to leave this open until the PR is accepted, MTS updated, and then the public servers updated/tested with the fix?

I pointed some users to this ticket to learn when they can use the tool again with this option.

Alternative - I can create an "check for update and test" for usegalaxy.org under https://github.com/galaxyproject/usegalaxy-playbook/issues and link back here and to my testing summary of items that are not immediately able to be resolved or are in my active to-do testing list https://github.com/galaxyproject/usegalaxy-playbook/issues/86. I plan to convert that into a Project - is getting unwieldly.

I don't specifically track update testing for usegalaxy.eu but often test there (and in a local) just to compare test results. I haven't been testing in Docker. Is there a repo you keep a track of that sort of thing (issues directly impacting the server)? Or, I could include both server tests in the playbook issues, when changes impact both servers, and test both at the same time.

Or better idea about how to coordinate around this? If there are open, clear, pending tests with existing test histories, this all is much easier to manage and allow others to also test/report back results in a central place. That's what I do in usegalaxy-playbook. I certainly don't want to make final integration testing too complicated - but a queue is nice and I've pretty much always used some version of that on every project I've worked on (whether I was doing the QA myself, or managing those that did) and decided to start using Github to keep track of issues just recently. Works great now, once in a Project will be super easy to manage it al. Note my lists are not comprehensive, the issues are mostly end-user focused (reported problems, or things we found ourselves that once adjusted, will make the Galaxy experience nicer :)

mvdbeek commented 6 years ago

It has been closed because the commit or PR contains the phrase Fixes #<number of issue>. Feel free to re-open at any time. I'd argue though that we're tracking development here, not deployments.