added dockerfile for pdata 1.28.1; corrected previous pangolin READMEs

kapsakcj commented 2 months ago

Simply updated the pangolin data version:

$ diff pangolin/4.3.1-pdata-1.28/Dockerfile pangolin/4.3.1-pdata-1.28.1/Dockerfile 
12c12
< ARG PANGOLIN_DATA_VER="v1.28"
---
> ARG PANGOLIN_DATA_VER="v1.28.1"

I also corrected a few spots in older Pangolin READMEs that had the incorrect pangolin-data version listed.

P-data 1.28.1 release notes here: https://github.com/cov-lineages/pangolin-data/releases/tag/v1.28.1

Removed annotation of KR.2 which was accidentally included in v1.28 as a child of LT.1 instead of being completely replaced by LT.1, causing most LT.1 sequences to be assigned KR.2. (See https://github.com/cov-lineages/pangolin-data/issues/60) No change to alias file, still pango-designation v1.28.

This version release addresses this bug ^

Pull Request (PR) checklist:

[x] Include a description of what is in this pull request in this message.
[x] 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 )
[x] 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)
- [x] (optional) All test files are located in same directory as the Dockerfile (i.e. shigatyper/2.0.1/test.sh)
[x] Create a simple container-specific README.md in the same directory as the Dockerfile (i.e. spades/3.12.0/README.md)
- [x] If this README is longer than 30 lines, there is an explanation as to why more detail was needed
[x] Dockerfile includes the recommended LABELS
[x] Main README.md has been updated to include the tool and/or version of the dockerfile(s) in this PR
[x] Program_Licenses.md contains the tool(s) used in this PR and has been updated for any missing

kapsakcj commented 2 months ago

I made the suggested change - tests succeeded as expected and the docker image is dramatically smaller. TY for the suggestion Kuluhan & Erin 👍

OK to merge and deploy? I would suggest using the image tag 4.3.1-pdata-1.28.1 to keep with our naming scheme. (and overwrite the latest tag)

Kincekara commented 2 months ago

Thank you, Curtis! The tests look good! I will merge and deploy this.

Kincekara commented 2 months ago

Deploy link: https://github.com/StaPH-B/docker-builds/actions/runs/9861690475

kapsakcj commented 2 months ago

TY!

kapsakcj commented 2 months ago

check out the (compressed) image size difference:

StaPH-B / docker-builds

added dockerfile for pdata 1.28.1; corrected previous pangolin READMEs #1017