Update Seqkit to 2.13.0

[cwoodside1278]

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/build-files/samtools/1.15 )
• Directory structure as name of the tool in lower case with special characters removed with a subdirectory of the version number in build-files (i.e. docker-builds/build-files/spades/3.12.0/Dockerfile)
  • (optional) All test files are located in same directory as the Dockerfile (i.e. build-files/shigatyper/2.0.1/test.sh)
• Create a simple container-specific README.md in the same directory as the Dockerfile (i.e. docker-builds/build-files/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

Description

Updated seqkit to 2.13.0 from 2.12.0

• created new directory structure seqkit/2.13.0
• changed noble from jammy
• Updated the container-specific read me to seqkit/2.13.0
• Updated the main read me to include the new version

Diff Output

I do not know what it is so big:

diff -r build-files/seqkit/2.12.0/Dockerfile build-files/seqkit/2.13.0/Dockerfile
1,53c1,54
< FROM ubuntu:jammy AS app
< 
< # ARG sets environment variables during the build stage
< ARG SEQKIT_VER="2.12.0"
< 
< # LABEL instructions tag the image with metadata that might be important to the user
< # Optional, but highly recommended
< LABEL base.image="ubuntu:jammy"
< LABEL dockerfile.version="1"
< LABEL software="SeqKit"
< LABEL software.version=${SEQKIT_VER}
< LABEL description="SeqKit - a cross-platform and ultrafast toolkit for FASTA/Q file manipulation"
< LABEL website="https://github.com/shenwei356/seqkit"
< LABEL license="https://github.com/shenwei356/seqkit/blob/master/LICENSE"
< LABEL maintainer="Henry Kunerth"
< LABEL maintainer.email="henrykunerth@gmail.com"
< LABEL maintainer2="Erin Young"
< LABEL maintainer2.email="eriny@utah.gov"
< 
< # Install dependences (update as needed)
< RUN apt-get update && apt-get install -y --no-install-recommends \
<       wget \
<       ca-certificates \
<       procps \
<       unzip && \
<       apt-get autoclean && rm -rf /var/lib/apt/lists/*
< 
< # download SEQKIT and organize directories
< RUN wget -q https://github.com/shenwei356/seqkit/releases/download/v${SEQKIT_VER}/seqkit_linux_amd64.tar.gz && \
<       tar -xzf seqkit_linux_amd64.tar.gz && \
<       mv seqkit /usr/local/bin/. && \
<       rm seqkit_linux_amd64.tar.gz && \
<       mkdir /data
< 
< # singularity compatibility
< ENV LC_ALL=C
< 
< CMD ["seqkit", "--help"]
< 
< # WORKDIR sets working directory
< WORKDIR /data
< 
< # A second FROM insruction creates a new stage
< # We use `test` for the test image
< FROM app AS test
< 
< WORKDIR /test
< 
< RUN seqkit --help
< 
< #download test .fasta and check that SEQKIT can run to generate stats
< RUN wget -q https://raw.githubusercontent.com/StaPH-B/docker-builds/master/tests/SARS-CoV-2/SRR13957123.consensus.fa && \
<       seqkit stat *
---
> FROM ubuntu:noble AS app
> 
> # ARG sets environment variables during the build stage
> ARG SEQKIT_VER="2.13.0"
> 
> # LABEL instructions tag the image with metadata that might be important to the user
> # Optional, but highly recommended
> 
> LABEL base.image="ubuntu:noble"
> LABEL dockerfile.version="1"
> LABEL software="SeqKit"
> LABEL software.version=${SEQKIT_VER}
> LABEL description="SeqKit - a cross-platform and ultrafast toolkit for FASTA/Q file manipulation"
> LABEL website="https://github.com/shenwei356/seqkit"
> LABEL license="https://github.com/shenwei356/seqkit/blob/master/LICENSE"
> LABEL maintainer="Henry Kunerth"
> LABEL maintainer.email="henrykunerth@gmail.com"
> LABEL maintainer2="Erin Young"
> LABEL maintainer2.email="eriny@utah.gov"
> 
> # Install dependences (update as needed)
> RUN apt-get update && apt-get install -y --no-install-recommends \
>       wget \
>       ca-certificates \
>       procps \
>       unzip && \
>       apt-get autoclean && rm -rf /var/lib/apt/lists/*
> 
> # download SEQKIT and organize directories
> RUN wget -q https://github.com/shenwei356/seqkit/releases/download/v${SEQKIT_VER}/seqkit_linux_amd64.tar.gz && \
>       tar -xzf seqkit_linux_amd64.tar.gz && \
>       mv seqkit /usr/local/bin/. && \
>       rm seqkit_linux_amd64.tar.gz && \
>       mkdir /data
> 
> # singularity compatibility
> ENV LC_ALL=C
> 
> CMD ["seqkit", "--help"]
> 
> # WORKDIR sets working directory
> WORKDIR /data
> 
> # A second FROM insruction creates a new stage
> # We use `test` for the test image
> FROM app AS test
> 
> WORKDIR /test
> 
> RUN seqkit --help
> 
> #download test .fasta and check that SEQKIT can run to generate stats
> RUN wget -q https://raw.githubusercontent.com/StaPH-B/docker-builds/master/tests/SARS-CoV-2/SRR13957123.consensus.fa && \
>       seqkit stat *
diff -r build-files/seqkit/2.12.0/README.md build-files/seqkit/2.13.0/README.md
1,36c1,36
< # SeqKit container
< 
< Main tool : [SeqKit](https://github.com/shenwei356/seqkit)
< 
< SeqKit is a cross-platform and ultrafast toolkit for FASTA/Q file manipulation.
< 
< Citation:
< 
< W Shen, S Le, Y Li*, F Hu*. SeqKit: a cross-platform and ultrafast toolkit for FASTA/Q file manipulation. PLOS ONE. doi:10.1371/journal.pone.0163962.
< 
< 
< - **Documents:** [http://bioinf.shenwei.me/seqkit](http://bioinf.shenwei.me/seqkit)
< ([**Usage**](http://bioinf.shenwei.me/seqkit/usage/),
< [**FAQ**](http://bioinf.shenwei.me/seqkit/faq/),
< [**Tutorial**](http://bioinf.shenwei.me/seqkit/tutorial/),
< and 
< [**Benchmark**](http://bioinf.shenwei.me/seqkit/benchmark/))
< 
< ## Example Usage
< 
< ```bash
< # get simple statistics from FASTA/Q files
< 
< seqkit stats <file name(s)>
< 
< # or with flags
< 
< seqkit stats --all --tabular <file name(s)>
< 
< # conversion from FASTA to FASTQ
< 
< seqkit fa2fq <file name(s)>
< 
< 
< 
< ```
---
> # SeqKit container
> 
> Main tool : [SeqKit](https://github.com/shenwei356/seqkit)
> 
> SeqKit is a cross-platform and ultrafast toolkit for FASTA/Q file manipulation.
> 
> Citation:
> 
> W Shen, S Le, Y Li*, F Hu*. SeqKit: a cross-platform and ultrafast toolkit for FASTA/Q file manipulation. PLOS ONE. doi:10.1371/journal.pone.0163962.
> 
> 
> - **Documents:** [http://bioinf.shenwei.me/seqkit](http://bioinf.shenwei.me/seqkit)
> ([**Usage**](http://bioinf.shenwei.me/seqkit/usage/),
> [**FAQ**](http://bioinf.shenwei.me/seqkit/faq/),
> [**Tutorial**](http://bioinf.shenwei.me/seqkit/tutorial/),
> and 
> [**Benchmark**](http://bioinf.shenwei.me/seqkit/benchmark/))
> 
> ## Example Usage
> 
> ```bash
> # get simple statistics from FASTA/Q files
> 
> seqkit stats <file name(s)>
> 
> # or with flags
> 
> seqkit stats --all --tabular <file name(s)>
> 
> # conversion from FASTA to FASTQ
> 
> seqkit fa2fq <file name(s)>
> 
> 
> 
> ```

Test Build

[+] Building 14.4s (11/11) FINISHED                                                                                                                                   docker:default
 => [internal] load build definition from Dockerfile                                                                                                                            0.0s
 => => transferring dockerfile: 1.71kB                                                                                                                                          0.0s
 => [internal] load metadata for docker.io/library/ubuntu:noble                                                                                                                 0.0s
 => [internal] load .dockerignore                                                                                                                                               0.0s
 => => transferring context: 2B                                                                                                                                                 0.0s
 => CACHED [app 1/4] FROM docker.io/library/ubuntu:noble@sha256:d1e2e92c075e5ca139d51a140fff46f84315c0fdce203eab2807c7e495eff4f9                                                0.0s
 => => resolve docker.io/library/ubuntu:noble@sha256:d1e2e92c075e5ca139d51a140fff46f84315c0fdce203eab2807c7e495eff4f9                                                           0.0s
 => [app 2/4] RUN apt-get update && apt-get install -y --no-install-recommends  wget  ca-certificates  procps  unzip &&  apt-get autoclean && rm -rf /var/lib/apt/lists/*      11.2s
 => [app 3/4] RUN wget -q https://github.com/shenwei356/seqkit/releases/download/v2.13.0/seqkit_linux_amd64.tar.gz &&  tar -xzf seqkit_linux_amd64.tar.gz &&  mv seqkit /usr/l  0.8s
 => [app 4/4] WORKDIR /data                                                                                                                                                     0.0s 
 => [test 1/3] WORKDIR /test                                                                                                                                                    0.0s 
 => [test 2/3] RUN seqkit --help                                                                                                                                                0.2s 
 => [test 3/3] RUN wget -q https://raw.githubusercontent.com/StaPH-B/docker-builds/master/tests/SARS-CoV-2/SRR13957123.consensus.fa &&  seqkit stat *                           0.4s 
 => exporting to image                                                                                                                                                          1.5s 
 => => exporting layers                                                                                                                                                         1.1s 
 => => exporting manifest sha256:adb7d5af30ee475a852db919278a08090598456cee0a5114068de1b246491bcc                                                                               0.0s 
 => => exporting config sha256:0c93481bd251cc3623cd99de4df43dfd5bb750839734c4f86cfd4df313913f37                                                                                 0.0s 
 => => exporting attestation manifest sha256:5689d76d122f7df18b6c8d26eda62239a807455da44f9eb32786cfedc7b03393                                                                   0.0s 
 => => exporting manifest list sha256:cb328f95d02e3fb61f3608a14600466bb19646e65a8fedee4da868f092b8938e                                                                          0.0s
 => => naming to docker.io/library/seqkit:2.13.0                                                                                                                                0.0s
 => => unpacking to docker.io/library/seqkit:2.13.0     

[erinyoung]

Tests worked

#11 [test 3/3] RUN wget -q https://raw.githubusercontent.com/StaPH-B/docker-builds/master/tests/SARS-CoV-2/SRR13957123.consensus.fa && 	seqkit stat *
#11 0.207 file                      format  type  num_seqs  sum_len  min_len  avg_len  max_len
#11 0.207 SRR13957123.consensus.fa  FASTA   DNA          1   29,778   29,778   29,778   29,778
#11 DONE 0.2s

[erinyoung]

I have no changes to recommend.

Thank you for putting this together!

I'll get this merged and deployed.

[erinyoung]

Thank you for putting this together. You can check the status of the deploy here: https://github.com/StaPH-B/docker-builds/actions/runs/23012873557