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adds dockerfile for pangolin 4.3.1 and pdata 1.23.1 #777

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merged 2 commits into from
Oct 27, 2023

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kapsakcj
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@kapsakcj kapsakcj commented Oct 27, 2023

PR adds a dockerfile & readme for a patch release of pangolin-data 1.23.1 which includes an important bugfix for calling BA.2.86.2, BA.2.86.3 and JQ.1. These were designated after pango-designation release 1.23, but accidentally included in the UShER lineageTree.pb tree. So previously when running pangolin on JQ.1 genomes, there would be an error since it was not included in the alias_key.json which is required by scorpio

I only want to announce this docker image and skip over the one that was just PR'd & deployed so that folks can avoid the bug with JQ.1 genomes

Changes from previous dockerfile:

  • added 2 tests
    • JN.2 (BA.2.86 sublineage); JN.2 is an alias of B.1.1.529.2.86.1.2
    • JQ.1 (BA.2.86.3 sublineage); JQ.1 is an alias of B.1.1.529.2.86.3.1

Thank you @erinyoung & the UPHL team for the JQ.1 genome!!! Very much appreciate you sharing the genome via gisaid & ncbi!

Pull Request (PR) checklist:

  • Include a description of what is in this pull request in this message.
  • The dockerfile successfully builds to a test target for the user creating the PR. (i.e. docker build --tag samtools:1.15test --target test docker-builds/samtools/1.15 )
  • Directory structure as name of the tool in lower case with special characters removed with a subdirectory of the version number (i.e. spades/3.12.0/Dockerfile)
    • (optional) All test files are located in same directory as the Dockerfile (i.e. shigatyper/2.0.1/test.sh)
  • Create a simple container-specific README.md in the same directory as the Dockerfile (i.e. spades/3.12.0/README.md)
    • If this README is longer than 30 lines, there is an explanation as to why more detail was needed
  • Dockerfile includes the recommended LABELS
  • Main README.md has been updated to include the tool and/or version of the dockerfile(s) in this PR
  • Program_Licenses.md contains the tool(s) used in this PR and has been updated for any missing

@@ -23,7 +23,7 @@ Additional tools:

This docker image contains `usher` version 0.6.2. This version of usher has a bug that can cause some lineage A samples to be assigned to A.* sublineages or even B or B.* sublineages.

If you are running `pangolin` on early 2020 sequences that may be lineage A, it is highly recommended to use the assignment cache (and upgrade to usher 0.6.3 when it is available) [See the pangolin-assignment v1.23 release page for more details](https://github.com/cov-lineages/pangolin-assignment/releases/tag/v1.23
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I see! It's missing the ")"

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@erinyoung erinyoung left a comment

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I have no changes to recommend.

Sorry for not catching the hyperlink error in the last version!

I have approved this PR, and I will let you push to dockerhub and quay

@erinyoung erinyoung merged commit d31e52a into master Oct 27, 2023
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@kapsakcj kapsakcj deleted the cjk-pdata-1.23.1 branch October 27, 2023 16:26
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thank you for the quick turnaround!! I will deploy now

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2 participants