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Add autoBIGS to IUC Toolshed #6799

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merged 17 commits into from
Feb 28, 2025
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RealYHD
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@RealYHD RealYHD commented Feb 24, 2025

Adds a Galaxy tool wrapper for autoBIGS.cli, a command line interface for batched sequence typing.


FOR CONTRIBUTOR:

  • I have read the CONTRIBUTING.md document and this tool is appropriate for the tools-iuc repo.
  • License permits unrestricted use (educational + commercial)
  • This PR adds a new tool or tool collection
  • This PR updates an existing tool or tool collection
  • This PR does something else (explain below)

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RealYHD commented Feb 26, 2025

@bgruening asides from waiting on the automatically fetched selection options for database names, does everything else look okay? If this is the case, may I request that the PR be merged? I have a pipeline process waiting on this tool's acceptance to IUC.

It looks to me #6799 (comment) should wait for bioconda/bioconda-recipes#54159 to be approved which I will implement into the Galaxy tool down the line if this is acceptable.

Thanks for the approval on the 0.6.0 release. I've updated the Galaxy tool XML. I unfortunately caught a bug with an optional argument that I need to use with Galaxy. I've fixed it as a release in 0.6.1 with it's PR at bioconda/bioconda-recipes#54170. After this PR is accepted, I'll run testing (automatic and manual) and push the changes.

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RealYHD commented Feb 27, 2025

I believe the latest commit (c2efa2b) fails because it depends on bioconda/bioconda-recipes#54197 (PR for autobigs-cli 0.6.2) being merged. Namely, I added the ability to use comma separated lists of FASTA. I can confirm, while using autobigs-cli 0.6.2 with a local installation of Galaxy through planemo, all tests past.

I've also added more tests to cover such use cases.

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RealYHD commented Feb 28, 2025

Thanks for approving of 0.6.2. As of c2efa2b, I am solely waiting for further review and approval of this PR.

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very nice! @RealYHD thanks a lot for considering all the crazy ideas ... :)

@bgruening bgruening merged commit 06d653e into galaxyproject:main Feb 28, 2025
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@RealYHD RealYHD deleted the autobigs branch February 28, 2025 17:47
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2 participants