adds dockerfile for pangolin 4.3.1 and pdata 1.23.1 #777
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…pecific readme and updates the main README.md table
erinyoung
reviewed
Oct 27, 2023
| @@ -23,7 +23,7 @@ Additional tools: | |||
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| 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. | |||
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| 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 ")"
erinyoung
approved these changes
Oct 27, 2023
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thank you for the quick turnaround!! I will deploy now |
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PR adds a dockerfile & readme for a patch release of
pangolin-data1.23.1 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 UShERlineageTree.pbtree. So previously when running pangolin on JQ.1 genomes, there would be an error since it was not included in thealias_key.jsonwhich is required byscorpioI 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:
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:
docker build --tag samtools:1.15test --target test docker-builds/samtools/1.15)spades/3.12.0/Dockerfile)shigatyper/2.0.1/test.sh)spades/3.12.0/README.md)