Add EMBOSS 6: fuzznuc #4347
Add EMBOSS 6: fuzznuc #4347
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The test failure says to check the artifacts but I don't see any... |
They are a bit hard to discover nowadays: click on "Summary" in the navigation bar on the left of the Action page. The Artifacts are at the very bottom of that section. |
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Maybe we can add a todo list to this old issue #65 .. keeping track of updating all the emboss tools?
tools/emboss/emboss_fuzznuc.xml
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| <tool id="emboss_fuzznuc37" name="fuzznuc" version="6.6.0"> | |||
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Can you use to version token here? And maybe rename to TOOL_VERSION?
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In there a reason for 37 in the id?
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sure, I have no idea why the 37. It was copied from emboss_5.
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Now I see. I did non get in the first place that you created a new folder.
With the change of the id we are destroying tool lineare (I guess) .. but keeping the space and upper case letters also seems to be no good option?
I guess we need someone here who knows better about tool lineage...
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This will be published to a new tool repo and will not have the same lineage as emboss_5.
The only way to have it in the same lineage would be to have emboss 6 in the emboss_5 repo.
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The only way to have it in the same lineage would be to have emboss 6 in the emboss_5 repo.
True, as far I as I understand, tool lineage is maintained only if also the ToolShed owner and repository name are the same (i.e. the whole guid minus the version).
This will be published to a new tool repo and will not have the same lineage as emboss_5.
As you've already noticed, 3 years ago I updated one tool in emboss_5 to v6.6.0 to keep the lineage. I see 2 alternative options here:
- Keep updating (or adding) tools in the
emboss_5directory.
Pros: preserve the lineage of the existing tools
Cons: theemboss_5repository becomes increasingly a misnomer; all-in-one repository - Create a new
emboss_suitesuite with a separate repository for each new/updated tool and sane tool IDS (like in this PR, but you would need to modified the.shed.ymllike in https://github.com/galaxyproject/tools-iuc/blob/master/tools/bcftools/.shed.yml )
Pros: one tool per repository; sane tool IDs; no "5" in the repo names
Cons: tool lineages broken, i.e. no clean upgrade path for workflows using these tools
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Is there value in a suite if it is all the same dependency?
I am not sure that there would be a clean upgrade path for workflows sticking with the emboss_5 repo. There are going to be a lot of incompatible changes in the major version bump of the tools.
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Is there value in a suite if it is all the same dependency?
I'll leave this one for @mvdbeek to reply :)
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Macros were copied forward from emboss_5 if anyone wants to reuse them for other tools. I can remove them if you think it isn't worth it.
Co-authored-by: M Bernt <m.bernt@ufz.de>
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
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What is the status here @nsoranzo and @bernt-matthias? This will be deployed as IUC. I guess the idea is to deprecate the |
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Main/Last question is tool lineage. Wondering if we can just mix versions in the old dir. Given that emboss has seen no updates in a long time (http://emboss.sourceforge.net/developers/changelog.html) we can hope that the tools will converge to the latest at one point. Has someone ever tried to bump emboss? |
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The old tools are all in one repo aren't they? |
yes
remember that there are barely any tests... |
It looks like people keep starting to implement automated EMBOSS 6 wrapper solutions but then abandoning them. I propose a more manual peace-meal approach based on interest.
I have created a new folder for emboss 6 given that the current emboss folder has its version number baked in. For future versions of emboss we can then reuse this folder. I have also removed special characters from the tool ID to improve compatibility with downstream scripts. The perl dependency was removed. I think it would be best to avoid extra dependencies if possible, removing the need for a special mulled container.
New parameters for fuzznuc have been included.
Some work should be done to remove the emboss_format_corrector.py but this appears like it might be non-trivial.emboss_format_corrector.py was outdated and removed
FOR CONTRIBUTOR:
Related #131