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Update nextstrain docker image for better mpox tree building #1704

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merged 1 commit into from
Aug 27, 2024

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vincent-czi
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Summary:

  • What: Update base nextstrain image; update ncov to avoid version conflicts

Notes:

  • Working document for this project: https://docs.google.com/document/d/16OYv9hdWTju9Lh14eRYKP-yxBUmL7W9EmePXeQcA00w/edit?pli=1#heading=h.uphcory1bhy9
  • Using latest mpox nextstrain snakemake workflow requires new version of Augur, possibly others. Seems best to update the docker image rather than updating tools per run in the shell script.
    • This will impact ncov snakemake workflow as well though, so updating it to current. Dan looked over our custom changes and they're not so important they beat getting up to date with where nextstrain is.
  • There will be subsequent work to update the mpox snakemake workflow.
  • Dan will be testing covid tree building in Staging after merge.

@vincent-czi vincent-czi added backend Involves changes to backend code ez-pz Quick and easy to review labels Aug 26, 2024
@vincent-czi vincent-czi requested a review from danrlu August 26, 2024 23:48
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@danrlu danrlu left a comment

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Thank you!

@danrlu danrlu merged commit c723b60 into trunk Aug 27, 2024
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@danrlu danrlu deleted the vince/update-nextstrain-image branch August 27, 2024 00:02
thanhleviet pushed a commit to theiagenghi/theiagenepi that referenced this pull request Sep 12, 2024
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