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adds stxtyper 1.0.27 dockerfile & readme; updates main readme with li…
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| FROM ubuntu:jammy AS app | ||
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| ARG STXTYPER_VER="1.0.27" | ||
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| LABEL base.image="ubuntu:jammy" | ||
| LABEL dockerfile.version="1" | ||
| LABEL software="stxtyper" | ||
| LABEL software.version="${STXTYPER_VER}" | ||
| LABEL description="Search for Shiga toxin genes within bacterial genome assemblies" | ||
| LABEL website="https://github.com/ncbi/stxtyper" | ||
| LABEL license="https://github.com/ncbi/stxtyper/blob/main/LICENSE" | ||
| LABEL maintainer="Curtis Kapsak" | ||
| LABEL maintainer.email="[email protected]" | ||
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| # install dependencies via apt; cleanup apt garbage | ||
| # blast from ubuntu:jammy is v2.12.0 (as of 2024-09-06) | ||
| # procps is for ps command (required for nextflow) | ||
| RUN apt-get update && apt-get install -y --no-install-recommends \ | ||
| wget \ | ||
| ca-certificates \ | ||
| ncbi-blast+ \ | ||
| procps && \ | ||
| apt-get autoclean && rm -rf /var/lib/apt/lists/* | ||
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| # download pre-compiled binary | ||
| RUN mkdir /stxtyper && \ | ||
| wget -q https://github.com/ncbi/stxtyper/releases/download/v${STXTYPER_VER}/stxtyper_v${STXTYPER_VER}_x86_64_Linux.tar.gz && \ | ||
| tar -xzf stxtyper_v${STXTYPER_VER}_x86_64_Linux.tar.gz --strip-components=1 -C /stxtyper && \ | ||
| rm -r stxtyper_v${STXTYPER_VER}_x86_64_Linux.tar.gz && \ | ||
| ls -lh /stxtyper | ||
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| # set PATH to include where stxtyper & fasta_check executables exist | ||
| ENV PATH="${PATH}:/stxtyper" \ | ||
| TERM=xterm-256color | ||
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| # set final working directory as /data for passing data in/out of container | ||
| WORKDIR /data | ||
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| FROM app AS test | ||
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| # print version and help options & run the supplied tests | ||
| RUN tblastn -version && \ | ||
| stxtyper --version && \ | ||
| stxtyper --help && \ | ||
| cd /stxtyper && \ | ||
| bash test_stxtyper.sh | ||
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| # download genome from NCBI and test stxtyper with it | ||
| # expect 1 perfect match to stx2o subtype, with COMPLETE operon designation | ||
| # https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_012224845.2/ | ||
| # grep below requires both strings to be present in the same line | ||
| RUN echo "downloading test genome & running through stxtyper..." && \ | ||
| wget -q https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/012/224/845/GCA_012224845.2_ASM1222484v2/GCA_012224845.2_ASM1222484v2_genomic.fna.gz && \ | ||
| stxtyper -n GCA_012224845.2_ASM1222484v2_genomic.fna.gz | tee test-result.tsv && \ | ||
| grep 'stx2o' test-result.tsv | grep 'COMPLETE' |
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| # stxtyper container | ||
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| Main tool: [stxtyper](https://github.com/ncbi/stxtyper) | ||
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| Additional tools: | ||
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| - ncbi-blast+ 2.12.0 | ||
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| Basic information on how to use this tool: | ||
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| - executable: `stxtyper` | ||
| - help: `stxtyper --help` | ||
| - version: `stxtyper --version` | ||
| - description: Detects and types Shiga toxin genes in nucleotide sequences | ||
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| Full documentation: [https://github.com/ncbi/stxtyper](https://github.com/ncbi/stxtyper) | ||
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| Note: [This software is now incorporated into NCBI's AMRFinderPlus software as of version 4.0.3](https://github.com/ncbi/amr/releases/tag/amrfinder_v4.0.3). Stxtyper will run under-the-hood of AMRFinderPlus when using the `amrfinder --organism Escherichia` option. | ||
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| ## Example Usage | ||
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| ```bash | ||
| # stxtyper accepts both gzipped and uncompressed FASTA files | ||
| stxtyper -n GCA_012224845.2_ASM1222484v2_genomic.fna.gz -o stxtyper-results.tsv | ||
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| $ column -t test-result.tsv | ||
| #target_contig stx_type operon identity target_start target_stop target_strand A_reference A_reference_subtype A_identity A_coverage B_reference B_reference_subtype B_identity B_coverage | ||
| CP113091.1 stx2o COMPLETE 100.00 2085533 2086768 + WAK52085.1 stxA2o 100.00 100.00 QZL10983.1 stxB2o 100.00 100.00 | ||
| ``` |