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| Original file line number | Diff line number | Diff line change |
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| ARG PBPTYPER_VERSION="2.0.0" | ||
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| FROM mambaorg/micromamba:1.5.8 as app | ||
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| # Version arguments | ||
| # ARG variables only persist during build time | ||
| ARG PBPTYPER_VERSION | ||
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| # build and run as root users since micromamba image has 'mambauser' set as the $USER | ||
| USER root | ||
| # set workdir to default for building; set to /data at the end | ||
| WORKDIR / | ||
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| LABEL base.image="mambaorg/micromamba:1.5.8" | ||
| LABEL dockerfile.version="1" | ||
| LABEL software="pbptyper" | ||
| LABEL software.version="${PBPTYPER_VERSION}" | ||
| LABEL description="In silico Penicillin Binding Protein (PBP) typer for Streptococcus pneumoniae assemblies" | ||
| LABEL website="https://github.com/rpetit3/pbptyper" | ||
| LABEL license="https://github.com/rpetit3/pbptyper/blob/main/LICENSE" | ||
| LABEL maintainer1="Curtis Kapsak" | ||
| LABEL maintainer1.email="[email protected]" | ||
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| # install dependencies; cleanup apt garbage | ||
| RUN apt-get update && apt-get install -y --no-install-recommends \ | ||
| wget \ | ||
| ca-certificates \ | ||
| procps && \ | ||
| apt-get autoclean && rm -rf /var/lib/apt/lists/* | ||
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| # Install pbptyper into the base conda/micromamba environment, pinning the version | ||
| # clean up conda garbage | ||
| RUN micromamba install --name base -c conda-forge -c bioconda -c defaults pbptyper=${PBPTYPER_VERSION} && \ | ||
| micromamba clean -a -y | ||
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| # set the environment, add base conda/micromamba bin directory into path | ||
| # set locale settings to UTF-8 | ||
| ENV PATH="/opt/conda/bin/:\ | ||
| ${PATH}" \ | ||
| LC_ALL=C.UTF-8 | ||
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| # set final working directory to /data | ||
| WORKDIR /data | ||
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| CMD pbptyper --help | ||
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| RUN pbptyper --help && \ | ||
| pbptyper --version | ||
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| # new base for testing | ||
| FROM app as test | ||
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| ARG PBPTYPER_VERSION | ||
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| # # so that all test inputs & outputs are kept in /test | ||
| WORKDIR /test | ||
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| # download test data from pbptyper repo | ||
| RUN wget -q https://github.com/rpetit3/pbptyper/archive/refs/tags/v${PBPTYPER_VERSION}.tar.gz && \ | ||
| tar -vxf v${PBPTYPER_VERSION}.tar.gz | ||
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| # shamelessly stolen and modified from https://github.com/rpetit3/pbptyper/blob/main/.github/workflows/test-pbptyper.yml (again) | ||
| RUN cd pbptyper-${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 && \ | ||
| cat SRR2912551.tsv && \ | ||
| head SRR2912551.tblastn.tsv && \ | ||
| echo "SRR8654742" && \ | ||
| 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 && \ | ||
| echo "not-spn" && \ | ||
| pbptyper --yaml data/pbptyper.yaml --targets data/pbptyper.fasta --input test/not-spn.fna.gz --prefix not-spn && \ | ||
| cat not-spn.tsv && \ | ||
| head not-spn.tblastn.tsv && \ | ||
| echo "not-a-fasta" && \ | ||
| pbptyper --yaml data/pbptyper.yaml --targets data/pbptyper.fasta --input test/not-a-fasta.fasta --prefix not-a-fasta && \ | ||
| cat not-a-fasta.tsv && \ | ||
| head not-a-fasta.tblastn.tsv && \ | ||
| echo "poor" && \ | ||
| 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 | ||
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| 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 |
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| # pbptyper container | ||
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| Main tool : [pbptyper](https://github.com/rpetit3/pbptyper) | ||
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| Full documentation: [https://github.com/rpetit3/pbptyper](https://github.com/rpetit3/pbptyper) | ||
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| In silico Penicillin Binding Protein (PBP) typer for Streptococcus pneumoniae assemblies | ||
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| ## Example Usage | ||
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| ```bash | ||
| # run pbptyper on an test S. pneumo assembly included with pbptyper | ||
| # WARNING: test data no longer included in docker image, visit here to get test data: https://github.com/rpetit3/pbptyper/tree/main/test | ||
| $ pbptyper --input SRR2912551.fna.gz --prefix SRR2912551 --db /pbptyper-*/db/ --outdir /SRR2912551-pbptyper-test | ||
| Running TBLASTN for 1A... | ||
| TBLASTN results written to /SRR2912551-pbptyper-test/SRR2912551-1A.tblastn.tsv | ||
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| Running TBLASTN for 2B... | ||
| TBLASTN results written to /SRR2912551-pbptyper-test/SRR2912551-2B.tblastn.tsv | ||
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| Running TBLASTN for 2X... | ||
| TBLASTN results written to /SRR2912551-pbptyper-test/SRR2912551-2X.tblastn.tsv | ||
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| Predicted PBP Type | ||
| ┏━━━━━━━━━━━━┳━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━┓ | ||
| ┃ sample ┃ pbptype ┃ 1A_coverage ┃ 1A_pident ┃ 2B_coverage ┃ 2B_pident ┃ 2X_coverage ┃ 2X_pident ┃ | ||
| ┡━━━━━━━━━━━━╇━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━┩ | ||
| │ SRR2912551 │ 23:0:2 │ 100 │ 100.000 │ 100 │ 100.000 │ 100 │ 100.000 │ | ||
| └────────────┴─────────┴─────────────┴───────────┴─────────────┴───────────┴─────────────┴───────────┘ | ||
| Predicted pbp type result written to /SRR2912551-pbptyper-test/SRR2912551.tsv | ||
| ``` |