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add BUSCO 5.4.7 #701

Merged
merged 9 commits into from
Aug 7, 2023
Merged

add BUSCO 5.4.7 #701

merged 9 commits into from
Aug 7, 2023

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Kincekara
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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

@Kincekara Kincekara marked this pull request as ready for review August 3, 2023 15:01
@Kincekara
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I used Focal as the base image to avoid Python errors on Jammy. Busco and other programs were not happy with later versions than Python 3.8. All functions of Busco work well on my tests.

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I added a test of running busco on a Salmonella genome and added the CMD layer.
@erinyoung
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It's looking good!

All your tests work. The labels are all there. It's going to be a great tool for the community.

What busco databases are included in this image?

I have some editing requests:

  • split the installation of your dependencies to different layers so that it's easier to read
  • add a version or commit (or something similar) for sepp and metaeuk when you download those tools
  • adjust the readme. It needs examples that reflect how you intend someone to use the image and shouldn't be a copy and paste of the help message of the tool.
  • Also, do you have pointers of how to mount a local database to a container based on the image this creates? If not, I'll likely have to come up with some text before this can get merged.

@Kincekara
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I believe all issues are resolved.

@erinyoung
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I think you have resolved all issues as well.

Thank you!

@erinyoung erinyoung self-requested a review August 7, 2023 16:54
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@erinyoung erinyoung left a comment

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I am going to

  1. merge this PR
  2. push to docker and quay using both the tag '5.4.7' and 'latest'

@erinyoung erinyoung merged commit 70f39ff into StaPH-B:master Aug 7, 2023
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@erinyoung
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You can track the stage of deployment at https://github.com/StaPH-B/docker-builds/actions/runs/5787821276

@Kincekara Kincekara deleted the new-docker-busco branch August 9, 2023 19:47
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2 participants