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Merge pull request #794 from StaPH-B/cjk-pasty-1.0.3
add pasty 1.0.3
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| ARG PASTY_VERSION="1.0.3" | ||
| # formatted for apt version syntax | ||
| ARG BLAST_VERSION="2.12.0+ds-3build1" | ||
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| FROM ubuntu:jammy as app | ||
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| # have to re-instatiate these variables | ||
| ARG PASTY_VERSION | ||
| ARG BLAST_VERSION | ||
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| LABEL base.image="ubuntu:jammy" | ||
| LABEL dockerfile.version="1" | ||
| LABEL software="pasty" | ||
| LABEL software.version="${PASTY_VERSION}" | ||
| LABEL description="In silico serogrouping of Pseudomonas aeruginosa isolates from genome assemblies" | ||
| LABEL website="https://github.com/rpetit3/pasty" | ||
| LABEL license="https://github.com/rpetit3/pasty/blob/main/LICENSE" | ||
| LABEL maintainer="Curtis Kapsak" | ||
| LABEL maintainer.email="[email protected]" | ||
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| # install dependencies | ||
| # ncbi-blast+ version in apt for ubuntu:jammy = v2.12.0 | ||
| # python v3.10.6 | ||
| RUN apt-get update && apt-get install -y --no-install-recommends \ | ||
| python3 \ | ||
| python3-pip \ | ||
| ncbi-blast+=${BLAST_VERSION} \ | ||
| wget \ | ||
| ca-certificates \ | ||
| procps && \ | ||
| apt-get autoclean && rm -rf /var/lib/apt/lists/* | ||
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| # install python deps | ||
| RUN pip3 install executor rich-click | ||
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| # download pasty; make /data | ||
| RUN echo "downloading pasty source code..." && \ | ||
| wget -q https://github.com/rpetit3/pasty/archive/refs/tags/v${PASTY_VERSION}.tar.gz && \ | ||
| tar -zxf v${PASTY_VERSION}.tar.gz && \ | ||
| rm -rf v${PASTY_VERSION}.tar.gz && \ | ||
| mkdir /data | ||
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| # set $PATH | ||
| # set perl locale settings for singularity compatibility | ||
| ENV PATH="${PATH}:/pasty-${PASTY_VERSION}/bin"\ | ||
| LC_ALL=C.UTF-8 | ||
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| # final working directory is /data | ||
| WORKDIR /data | ||
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| # testing layer starts here | ||
| FROM app as test | ||
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| # re-instatiate for use below in test layer | ||
| ARG PASTY_VERSION | ||
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| # running the below test commands from the root pasty directory | ||
| WORKDIR /pasty-${PASTY_VERSION} | ||
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| # shamelessly stolen and modified from https://github.com/rpetit3/pasty/blob/main/.github/workflows/test-pasty.yml | ||
| RUN echo "O1-GCF_000504045" && \ | ||
| pasty --assembly test/O1-GCF_000504045.fna.gz --prefix O1-GCF_000504045 && \ | ||
| cat O1-GCF_000504045.tsv && \ | ||
| cat O1-GCF_000504045.details.tsv && \ | ||
| echo "O2-GCF_000006765" && \ | ||
| pasty --assembly test/O2-GCF_000006765.fna.gz --prefix O2-GCF_000006765 --outdir O2 && \ | ||
| cat O2/O2-GCF_000006765.tsv && \ | ||
| cat O2/O2-GCF_000006765.details.tsv && \ | ||
| echo "O3-GCF_000271365" && \ | ||
| pasty --assembly test/O3-GCF_000271365.fna.gz --prefix O3-GCF_000271365 --outdir O3 && \ | ||
| cat O3/O3-GCF_000271365.tsv && \ | ||
| cat O3/O3-GCF_000271365.details.tsv && \ | ||
| echo "O4-GCF_024652945" && \ | ||
| pasty --assembly test/O4-GCF_024652945.fna.gz --prefix O4-GCF_024652945 --outdir O4 && \ | ||
| cat O4/O4-GCF_024652945.tsv && \ | ||
| cat O4/O4-GCF_024652945.details.tsv && \ | ||
| echo "O6-GCF_001457615" && \ | ||
| pasty --assembly test/O6-GCF_001457615.fna.gz --prefix O6-GCF_001457615 && \ | ||
| cat O6-GCF_001457615.tsv && \ | ||
| cat O6-GCF_001457615.details.tsv && \ | ||
| echo "O7-GCF_001482325" && \ | ||
| pasty --assembly test/O7-GCF_001482325.fna.gz --prefix O7-GCF_001482325 && \ | ||
| cat O7-GCF_001482325.tsv && \ | ||
| cat O7-GCF_001482325.details.tsv && \ | ||
| echo "O9-GCF_002075065" && \ | ||
| pasty --assembly test/O9-GCF_002075065.fna.gz --prefix O9-GCF_002075065 && \ | ||
| cat O9-GCF_002075065.tsv && \ | ||
| cat O9-GCF_002075065.details.tsv && \ | ||
| echo "O10-GCF_009676765" && \ | ||
| pasty --assembly test/O10-GCF_009676765.fna.gz --prefix O10-GCF_009676765 && \ | ||
| cat O10-GCF_009676765.tsv && \ | ||
| cat O10-GCF_009676765.details.tsv && \ | ||
| echo "O11-GCF_002192495" && \ | ||
| pasty --assembly test/O11-GCF_002192495.fna.gz --prefix O11-GCF_002192495 && \ | ||
| cat O11-GCF_002192495.tsv && \ | ||
| cat O11-GCF_002192495.details.tsv && \ | ||
| echo "O12-GCF_000981825" && \ | ||
| pasty --assembly test/O12-GCF_000981825.fna.gz --prefix O12-GCF_000981825 && \ | ||
| cat O12-GCF_000981825.tsv && \ | ||
| cat O12-GCF_000981825.details.tsv && \ | ||
| echo "NT-GCF_000292685" && \ | ||
| pasty --assembly test/NT-GCF_000292685.fna.gz --prefix NT-GCF_000292685 && \ | ||
| cat NT-GCF_000292685.tsv && \ | ||
| cat NT-GCF_000292685.details.tsv && \ | ||
| echo "empty" && \ | ||
| pasty --assembly test/empty.fasta --prefix empty && \ | ||
| cat empty.tsv && \ | ||
| cat empty.details.tsv && \ | ||
| echo "not-a-fasta" && \ | ||
| pasty --assembly test/not-a-fasta.fasta --prefix not-a-fasta && \ | ||
| cat not-a-fasta.tsv && \ | ||
| cat not-a-fasta.details.tsv && \ | ||
| echo "poor" && \ | ||
| pasty --assembly test/poor.fasta --prefix poor --outdir poor && \ | ||
| cat poor/poor.tsv && \ | ||
| cat poor/poor.details.tsv && \ | ||
| echo "O2-GCF_001444895-int-bug" && \ | ||
| pasty --assembly test/O2-GCF_001444895-int-bug.fna.gz --prefix O2-GCF_001444895-int-bug --outdir O2 && \ | ||
| cat O2/O2-GCF_001444895-int-bug.tsv && \ | ||
| cat O2/O2-GCF_001444895-int-bug.details.tsv | ||
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| # print help and version info | ||
| RUN pasty --help && \ | ||
| pasty --version && \ | ||
| pasty --check |
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| # pasty container | ||
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| Main tool : [pasty](https://github.com/rpetit3/pasty) | ||
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| Additional tools: | ||
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| - ncbi-blast+ 2.12.0 | ||
| - python 3.10.12 | ||
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| Full documentation: [https://github.com/rpetit3/pasty](https://github.com/rpetit3/pasty) | ||
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| A tool easily taken advantage of for in silico serogrouping of Pseudomonas aeruginosa isolates from genome assemblies | ||
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| ## Example Usage | ||
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| ```bash | ||
| # test genome assemblies are included in the docker image at /pasty-1.0.2/test/ | ||
| # visit here to see more information: https://github.com/rpetit3/pasty/tree/main/test | ||
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| # run pasty via docker container (command broken into 2 lines for readability) | ||
| $ docker run --rm -v $PWD:/data -u $(id -u):$(id -g) staphb/pasty:1.0.2 \ | ||
| pasty --assembly /pasty-1.0.2/test/O1-GCF_000504045.fna.gz --prefix O1-GCF_000504045 | ||
| Running pasty with following parameters: | ||
| --assembly /pasty-1.0.2/test/O1-GCF_000504045.fna.gz | ||
| --db /pasty-1.0.2/db/OSAdb.fasta | ||
| --prefix O1-GCF_000504045 | ||
| --outdir ./ | ||
| --min_pident 95 | ||
| --min_coverage 95 | ||
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| Running BLASTN... | ||
| Writing outputs... | ||
| BLASTN results written to ./O1-GCF_000504045.blastn.tsv | ||
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| Serogroup Results | ||
| ┏━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━┳━━━━━━━━━━┳━━━━━━━━━━━┓ | ||
| ┃ sample ┃ serogroup ┃ coverage ┃ fragments ┃ | ||
| ┡━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━╇━━━━━━━━━━╇━━━━━━━━━━━┩ | ||
| │ O1-GCF_000504045 │ O1 │ 99.97 │ 1 │ | ||
| │ O1-GCF_000504045 │ O2 │ 9.83 │ 2 │ | ||
| │ O1-GCF_000504045 │ O3 │ 11.18 │ 2 │ | ||
| │ O1-GCF_000504045 │ O4 │ 14.36 │ 2 │ | ||
| │ O1-GCF_000504045 │ O5 │ 0 │ 0 │ | ||
| │ O1-GCF_000504045 │ O6 │ 14.07 │ 2 │ | ||
| │ O1-GCF_000504045 │ O7 │ 11.54 │ 2 │ | ||
| │ O1-GCF_000504045 │ O9 │ 36.62 │ 1 │ | ||
| │ O1-GCF_000504045 │ O10 │ 12.52 │ 2 │ | ||
| │ O1-GCF_000504045 │ O11 │ 15.85 │ 2 │ | ||
| │ O1-GCF_000504045 │ O12 │ 1.24 │ 1 │ | ||
| │ O1-GCF_000504045 │ O13 │ 15.39 │ 2 │ | ||
| │ O1-GCF_000504045 │ WyzB │ 0 │ 0 │ | ||
| └──────────────────┴───────────┴──────────┴───────────┘ | ||
| Serogroup Results written to ./O1-GCF_000504045.details.tsv | ||
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| Predicted Serogroup | ||
| ┏━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━┳━━━━━━━━━━┳━━━━━━━━━━━┳━━━━━━━━━┓ | ||
| ┃ sample ┃ serogroup ┃ coverage ┃ fragments ┃ comment ┃ | ||
| ┡━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━╇━━━━━━━━━━╇━━━━━━━━━━━╇━━━━━━━━━┩ | ||
| │ O1-GCF_000504045 │ O1 │ 99.97 │ 1 │ │ | ||
| └──────────────────┴───────────┴──────────┴───────────┴─────────┘ | ||
| Predicted serogroup result written to ./O1-GCF_000504045.tsv | ||
| ``` |