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adds pangolin 4.3.1 & pdata 1.24 #851

Merged
merged 2 commits into from
Jan 22, 2024
Merged

adds pangolin 4.3.1 & pdata 1.24 #851

merged 2 commits into from
Jan 22, 2024

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kapsakcj
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@kapsakcj kapsakcj commented Jan 22, 2024

Adds new dockerfile for pangolin v4.3.1 and new version of pangolin-data v1.24

I used the previous dockerfile pangolin/4.3.1-pdata-1.23.1-1/Dockerfile as the starting point that includes Erin's changes for the env variable XDG_CACHE_HOME added in PR #812

Changes from previous dockerfile are minor. only updated line 12 for pangolin-data version and updated 2 comments:

$ diff pangolin/4.3.1-pdata-1.23.1-1/Dockerfile pangolin/4.3.1-pdata-1.24/Dockerfile
12c12
< ARG PANGOLIN_DATA_VER="v1.23.1"
---
> ARG PANGOLIN_DATA_VER="v1.24"
71a72
> # final working directory in "app" layer is /data for passing data in/out of container
77c78
< # default command is to pull up help options for virulencefinder; can be overridden of course
---
> # default command is to pull up help options for pangolin; can be overridden of course

I propose this as the docker image name & tag staphb/pangolin:4.3.1-pdata-1.24 and the :latest tag overwritten as usual.

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

@kapsakcj kapsakcj marked this pull request as ready for review January 22, 2024 17:15
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@erinyoung erinyoung left a comment

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I have no changes to recommend.

I'm going to

  1. merge this PR
  2. deploy to dockerhub and quay using the tag '4.3.1-pdata-1.24'
  3. overwrite the 'latest' tag

@erinyoung erinyoung merged commit 9579e05 into master Jan 22, 2024
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@erinyoung
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Thank you for putting this together!

You can check the status of the deploy at https://github.com/StaPH-B/docker-builds/actions/runs/7615331876

@kapsakcj kapsakcj deleted the cjk-pdata-1.24 branch January 22, 2024 18:01
@kapsakcj
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thank you for the lightning fast review 🎉

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2 participants