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adding genomad version 1.8.1 #1090

Merged
merged 1 commit into from
Oct 31, 2024
Merged

adding genomad version 1.8.1 #1090

merged 1 commit into from
Oct 31, 2024

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erinyoung
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@erinyoung erinyoung commented Oct 29, 2024

There's a new version of genomad!

According to the release notes, this has some bug fixes and some performance changes.

I changed

  • ARG GENOMAD_VER to 1.8.1
  • added --no-cache-dir to the pip install layer
  • updated the database comment to signify that the database is version 1.7
  • added a newline to a test line
 $ diff genomad/1.8*/Dockerfile
2c2
< ARG GENOMAD_VER="1.8.0"
---
> ARG GENOMAD_VER="1.8.1"
55c55
<     python3 -m pip install v${GENOMAD_VER}.tar.gz && \
---
>     python3 -m pip install --no-cache-dir v${GENOMAD_VER}.tar.gz && \
61,62c61,62
< # downloads latest database, which is version 1.6 and about ~1.6 G in size
< RUN genomad download-database .
---
> # downloads latest database, which is version 1.7 and about ~1.6 G in size
> RUN genomad download-database . 
81c81,82
< RUN pip list && wget -q https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/025/259/185/GCA_025259185.1_ASM2525918v1/GCA_025259185.1_ASM2525918v1_genomic.fna.gz && \
---
> RUN pip list && \
>     wget -q https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/025/259/185/GCA_025259185.1_ASM2525918v1/GCA_025259185.1_ASM2525918v1_genomic.fna.gz && \

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 merged commit 684500b into master Oct 31, 2024
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@Kincekara
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Thank you for the update!
Deploy link: https://github.com/StaPH-B/docker-builds/actions/runs/11612751295

@erinyoung erinyoung deleted the erin-genomad branch December 9, 2024 19:35
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2 participants