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add gfastats version 1.3.7 #943

Merged
merged 3 commits into from
Jun 6, 2024
Merged

add gfastats version 1.3.7 #943

merged 3 commits into from
Jun 6, 2024

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erinyoung
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There's a new version of gfastats! Nothing is listed in the release notes (https://github.com/vgl-hub/gfastats/releases/tag/v1.3.7), but I'm sure there's new features or bug fixes.

The file that used to get download and built is no longer available, so this uses the pre-built executable.

All the differences between the prior file and 1.3.7

$ diff gfastats/1.3.6/Dockerfile gfastats/1.3.7/Dockerfile 
0a1,2
> ARG GFASTATS_VER=1.3.7
> 
3c5
< ARG GFASTATS_VER=1.3.6
---
> ARG GFASTATS_VER
21c23,24
<   zlib1g-dev && \
---
>   zlib1g-dev \
>   unzip && \
24,28c27,32
< RUN wget -q https://github.com/vgl-hub/gfastats/releases/download/v${GFASTATS_VER}/gfastats.v${GFASTATS_VER}.tar.gz && \
<   tar -xf gfastats.v${GFASTATS_VER}.tar.gz && \
<   rm gfastats.v${GFASTATS_VER}.tar.gz && \
<   cd /gfastats && \
<   make -j
---
> WORKDIR /usr/local/bin
> 
> RUN wget -q https://github.com/vgl-hub/gfastats/releases/download/v${GFASTATS_VER}/gfastats.v${GFASTATS_VER}-linux.zip && \
>   unzip gfastats.v${GFASTATS_VER}-linux.zip && \
>   rm gfastats.v${GFASTATS_VER}-linux.zip && \
>   chmod +x gfastats
30c34
< ENV PATH="/gfastats/build/bin:${PATH}" \
---
> ENV PATH="$PATH" \
32a37,38
> CMD gfastats --help
> 
36a43,44
> ARG GFASTATS_VER
> 
41,44c49,56
< RUN gfastats /gfastats/testFiles/random1.fasta -o gfa && \
<   gfastats /gfastats/testFiles/random2.gfa2 && \
<   gfastats /gfastats/testFiles/random1.fasta -k /gfastats/testFiles/random1.instructions.sak -o gfa && \
<   gfastats --tabular --seq-report /gfastats/testFiles/random6.circular.gfa
\ No newline at end of file
---
> RUN wget -q https://github.com/vgl-hub/gfastats/archive/refs/tags/v${GFASTATS_VER}.tar.gz && \
>   tar -xvf v${GFASTATS_VER}.tar.gz
> 
> RUN gfastats gfastats-${GFASTATS_VER}/testFiles/random1.fasta -o gfa && \
>   gfastats gfastats-${GFASTATS_VER}/testFiles/random2.gfa2 && \
>   gfastats gfastats-${GFASTATS_VER}/testFiles/random1.fasta -k gfastats-${GFASTATS_VER}/testFiles/random1.instructions.sak -o gfa && \
>   gfastats --tabular --seq-report gfastats-${GFASTATS_VER}/testFiles/random6.circular.gfa
>   
\ No newline at end of file

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 20a682a into master Jun 6, 2024
2 checks passed
@Kincekara
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Thank you for the update!
Deploy link: https://github.com/StaPH-B/docker-builds/actions/runs/9401614696

@erinyoung erinyoung deleted the erin-gfastats branch June 6, 2024 16:09
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2 participants