adding pbptyper version 2.0.0

[erinyoung]

There's a new version of pbptyper!

According to the release notes, pbptyper now uses camlhmp and there are likely other small changes and bug fixes.

The usage for pbptyper has changed, so I updated the tests and readme as well.

The full diff:

$ diff pbptyper/1.0.4/Dockerfile pbptyper/2.0.0/Dockerfile 
1c1,3
< FROM mambaorg/micromamba:0.24.0 as app
---
> ARG PBPTYPER_VERSION="2.0.0"
> 
> FROM mambaorg/micromamba:1.5.8 as app
5c7
< ARG PBPTYPER_VERSION="1.0.4"
---
> ARG PBPTYPER_VERSION
12c14
< LABEL base.image="mambaorg/micromamba:0.24.0"
---
> LABEL base.image="mambaorg/micromamba:1.5.8"
24,27c26,29
<  wget \
<  ca-certificates \
<  procps && \
<  apt-get autoclean && rm -rf /var/lib/apt/lists/*
---
>     wget \
>     ca-certificates \
>     procps && \
>     apt-get autoclean && rm -rf /var/lib/apt/lists/*
32c34
<  micromamba clean -a -y
---
>     micromamba clean -a -y
38c40
<  LC_ALL=C.UTF-8
---
>     LC_ALL=C.UTF-8
42a45,50
> CMD pbptyper --help
> 
> RUN pbptyper --help && \
>     pbptyper --version
> 
> 
46,48c54
< # # so that mamba/conda env is active when running below commands
< ENV ENV_NAME="base"
< ARG MAMBA_DOCKERFILE_ACTIVATE=1
---
> ARG PBPTYPER_VERSION
52a59
> 
54,63c61,71
< RUN wget https://github.com/rpetit3/pbptyper/raw/main/test/SRR2912551.fna.gz && \
<     wget https://github.com/rpetit3/pbptyper/raw/main/test/SRR8654742.fna && \
<     wget https://github.com/rpetit3/pbptyper/blob/main/test/empty.fasta && \
<     wget https://github.com/rpetit3/pbptyper/blob/main/test/not-a-fasta.fasta && \
<     wget https://github.com/rpetit3/pbptyper/blob/main/test/not-spn.fna.gz && \
<     wget https://github.com/rpetit3/pbptyper/blob/main/test/poor.fasta
< 
< # shamelessly stolen and modified from https://github.com/rpetit3/pbptyper/blob/main/.github/workflows/test-pbptyper.yml
< RUN echo "SRR2912551" && \
<     pbptyper --assembly /test/SRR2912551.fna.gz --prefix SRR2912551 && \
---
> RUN wget -q https://github.com/rpetit3/pbptyper/archive/refs/tags/v${PBPTYPER_VERSION}.tar.gz && \
>     tar -vxf v${PBPTYPER_VERSION}.tar.gz
>     
> # shamelessly stolen and modified from https://github.com/rpetit3/pbptyper/blob/main/.github/workflows/test-pbptyper.yml (again)
> RUN cd pbptyper-${PBPTYPER_VERSION} && \
>     echo "ERR1065617" && \
>     pbptyper --yaml data/pbptyper.yaml --targets data/pbptyper.fasta --input test/ERR1065617.fna.gz --prefix ERR1065617 && \
>     cat ERR1065617.tsv && \
>     head ERR1065617.tblastn.tsv && \
>     echo "SRR2912551" && \
>     pbptyper --yaml data/pbptyper.yaml --targets data/pbptyper.fasta --input test/SRR2912551.fna.gz --prefix SRR2912551 && \
65,67c73
<     head SRR2912551-1A.tblastn.tsv && \
<     head SRR2912551-2B.tblastn.tsv && \
<     head SRR2912551-2X.tblastn.tsv && \
---
>     head SRR2912551.tblastn.tsv && \
69,73c75,89
<     pbptyper --assembly /test/SRR8654742.fna --prefix SRR8654742 && \
<     cat SRR8654742.tsv && \
<     head SRR8654742-1A.tblastn.tsv && \
<     head SRR8654742-2B.tblastn.tsv && \
<     head SRR8654742-2X.tblastn.tsv && \
---
>     pbptyper --yaml data/pbptyper.yaml --targets data/pbptyper.fasta --input test/SRR8654742.fna --prefix SRR8654742 --outdir SRR8654742 && \
>     cat SRR8654742/SRR8654742.tsv && \
>     head SRR8654742/SRR8654742.tblastn.tsv && \
>     echo "S. pseudopneumoniae" && \
>     pbptyper --yaml data/pbptyper.yaml --targets data/pbptyper.fasta --input test/spseudopneumoniae.fna.gz --prefix spseudopneumoniae --outdir spseudopneumoniae && \
>     cat spseudopneumoniae/spseudopneumoniae.tsv && \
>     head spseudopneumoniae/spseudopneumoniae.tblastn.tsv && \
>     echo "S. mitis" && \
>     pbptyper --yaml data/pbptyper.yaml --targets data/pbptyper.fasta --input test/smitis.fna.gz --prefix smitis --outdir smitis && \
>     cat smitis/smitis.tsv && \
>     head smitis/smitis.tblastn.tsv && \
>     echo "S. suis" && \
>     pbptyper --yaml data/pbptyper.yaml --targets data/pbptyper.fasta --input test/ssuis.fna.gz --prefix ssuis --outdir ssuis && \
>     cat ssuis/ssuis.tsv && \
>     head ssuis/ssuis.tblastn.tsv && \
75c91
<     pbptyper --assembly /test/not-spn.fna.gz --prefix not-spn && \
---
>     pbptyper --yaml data/pbptyper.yaml --targets data/pbptyper.fasta --input test/not-spn.fna.gz --prefix not-spn && \
77,85c93
<     head not-spn-1A.tblastn.tsv && \
<     head not-spn-2B.tblastn.tsv && \
<     head not-spn-2X.tblastn.tsv && \
<     echo "empty" && \
<     pbptyper --assembly /test/empty.fasta --prefix empty && \
<     cat empty.tsv && \
<     head empty-1A.tblastn.tsv && \
<     head empty-2B.tblastn.tsv && \
<     head empty-2X.tblastn.tsv && \
---
>     head not-spn.tblastn.tsv && \
87c95
<     pbptyper --assembly /test/not-a-fasta.fasta --prefix not-a-fasta && \
---
>     pbptyper --yaml data/pbptyper.yaml --targets data/pbptyper.fasta --input test/not-a-fasta.fasta --prefix not-a-fasta && \
89,91c97
<     head not-a-fasta-1A.tblastn.tsv && \
<     head not-a-fasta-2B.tblastn.tsv && \
<     head not-a-fasta-2X.tblastn.tsv && \
---
>     head not-a-fasta.tblastn.tsv && \
93,102c99,107
<     pbptyper --assembly /test/poor.fasta --prefix poor && \
<     cat poor.tsv && \
<     head poor-1A.tblastn.tsv && \
<     head poor-2B.tblastn.tsv && \
<     head poor-2X.tblastn.tsv
< 
< # print help and version info; check dependencies
< RUN pbptyper --help && \
<  pbptyper --check && \
<  pbptyper --version
---
>     pbptyper --yaml data/pbptyper.yaml --targets data/pbptyper.fasta --input test/poor.fasta --prefix poor --outdir poor && \
>     cat poor/poor.tsv && \
>     head poor/poor.tblastn.tsv
> 
> RUN cd pbptyper-${PBPTYPER_VERSION} && \
>     echo "ERR1065617 again" && \
>     pbptyper --input test/ERR1065617.fna.gz --prefix ERR1065617_2 && \
>     cat ERR1065617_2.tsv && \
>     head ERR1065617_2.tblastn.tsv
\ 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]

Thank you for putting all these together!
You can check the image deployment here: https://github.com/StaPH-B/docker-builds/actions/runs/11150466931.