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Adding kleborate version 3.1.2 (#1092)
* adding kleborate version 3.0.0 * adding kleborate version 3.1.2 * removed extra comments * removed git * fixed extra path * silenced some warnings; updated some comments; updated CMD to recommended format; uninstall old version of mash installed automatically via pypi since we install it manually * removed inaccurate comment --------- Co-authored-by: Curtis Kapsak <[email protected]>
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| FROM ubuntu:jammy AS app | ||
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| # for easy upgrade later. ARG variables only persist during image build time | ||
| ARG KLEBORATE_VER="3.1.2" | ||
| ARG MINIMAP2_VER="2.28" | ||
| ARG MASH_VER="2.3" | ||
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| LABEL base.image="ubuntu:jammy" | ||
| LABEL dockerfile.version="1" | ||
| LABEL software="Kleborate" | ||
| LABEL software.version="${KLEBORATE_VER}" | ||
| LABEL description="tool to screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC)" | ||
| LABEL website="https://github.com/katholt/Kleborate" | ||
| LABEL license="https://github.com/katholt/Kleborate/blob/master/LICENSE" | ||
| LABEL maintainer="Curtis Kapsak" | ||
| LABEL maintainer.email="[email protected]" | ||
| LABEL maintainer2="Frank Ambrosio" | ||
| LABEL maintainer2.email="[email protected]" | ||
| LABEL maintainer3="Erin Young" | ||
| LABEL maintainer3.email="[email protected]" | ||
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| # install prerequisites. Cleanup apt garbage | ||
| RUN apt-get update && apt-get install -y --no-install-recommends \ | ||
| python3 \ | ||
| python3-pip \ | ||
| wget \ | ||
| ca-certificates \ | ||
| bzip2 \ | ||
| procps \ | ||
| curl && \ | ||
| rm -rf /var/lib/apt/lists/* && apt-get autoclean | ||
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| # mash; update UID and GID of mash files; make /data | ||
| # UID and GID changes because the original owner is UID: 1081147385 and GID: 1360859114 which does NOT play well with systems that limits GIDs and UIDs | ||
| RUN wget -q https://github.com/marbl/Mash/releases/download/v${MASH_VER}/mash-Linux64-v${MASH_VER}.tar && \ | ||
| tar -xvf mash-Linux64-v${MASH_VER}.tar --no-same-owner && \ | ||
| rm -rf mash-Linux64-v${MASH_VER}.tar && \ | ||
| chown root:root /mash-Linux64-v${MASH_VER}/* | ||
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| # install minimap2 binary | ||
| RUN curl -L https://github.com/lh3/minimap2/releases/download/v${MINIMAP2_VER}/minimap2-${MINIMAP2_VER}_x64-linux.tar.bz2 | \ | ||
| tar -jxvf - --no-same-owner | ||
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| # set PATH | ||
| ENV PATH="/mash-Linux64-v${MASH_VER}:/minimap2-${MINIMAP2_VER}_x64-linux:${PATH}" | ||
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| # install kleborate; uninstall mash (that comes with kleborate via pypi, see: https://github.com/klebgenomics/Kleborate/issues/90); make /data | ||
| RUN pip install --no-cache-dir kleborate==${KLEBORATE_VER} && \ | ||
| pip uninstall mash -y && \ | ||
| mkdir /data | ||
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| # set working directory | ||
| WORKDIR /data | ||
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| CMD [ "kleborate", "--help" ] | ||
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| FROM app AS test | ||
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| WORKDIR /test | ||
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| # from https://kleborate.readthedocs.io/en/latest/Installation.html | ||
| RUN wget -q https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/002/813/595/GCF_002813595.1_ASM281359v1/GCF_002813595.1_ASM281359v1_genomic.fna.gz && \ | ||
| kleborate -a GCF_002813595.1_ASM281359v1_genomic.fna.gz -o kleborate_test -p kpsc && \ | ||
| head kleborate_test/klebsiella_pneumo_complex_output.txt | ||
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| # print help and version info | ||
| RUN kleborate --help && kleborate --version && kleborate --list_modules |
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| # Kleborate container | ||
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| Main tool : [Kleborate](https://github.com/katholt/Kleborate) | ||
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| :warning: **Note:** Kleborate v3 is different from v2, please see here for the differences: https://kleborate.readthedocs.io/en/latest/index.html#changes-from-v2 | ||
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| Additional tools: | ||
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| - [mash](https://github.com/marbl/Mash) version 2.3 | ||
| - [minimap2](https://github.com/lh3/minimap2) version 2.28 | ||
| - [kaptive](https://github.com/klebgenomics/Kaptive) version 3.0.0b6 | ||
| - biopython 1.84 | ||
| - dna-features-viewer 3.1.3 | ||
| - matplotlib 3.9.2 | ||
| - numpy 2.1.3 | ||
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| Full documentation: [https://github.com/katholt/Kleborate/wiki](https://github.com/katholt/Kleborate/wiki) | ||
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| Description: | ||
| > Kleborate is a tool to screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC) for: | ||
| > | ||
| > - MLST sequence type | ||
| > - species (e.g. K. pneumoniae, K. quasipneumoniae, K. variicola, etc.) | ||
| > - ICEKp associated virulence loci: yersiniabactin (ybt), colibactin (clb), salmochelin (iro), hypermucoidy (rmpA) | ||
| > - virulence plasmid associated loci: salmochelin (iro), aerobactin (iuc), hypermucoidy (rmpA, rmpA2) | ||
| > - antimicrobial resistance determinants: acquired genes, SNPs, gene truncations and intrinsic β-lactamases | ||
| > - K (capsule) and O antigen (LPS) serotype prediction, via wzi alleles and Kaptive | ||
| ## Included models | ||
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| Kleborate has models for both Klebsiella and Escherichia species. The available presets and models are listed below. | ||
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| Available presets: kpsc, kosc, escherichia | ||
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| ``` | ||
| Available modules for Kleborate | ||
| ------------------------------- | ||
| enterobacterales__species: Mash-based species detection for enterobacterales species | ||
| escherichia__mlst_achtman: chromosomal MLST for Escherichia coli using the Achtman scheme | ||
| escherichia__mlst_pasteur: chromosomal MLST for Escherichia coli using the Pasteur scheme | ||
| general__contig_stats: basic stats on the assembly's contigs | ||
| klebsiella__abst: MLST on the KpSC aerobactin locus (iuc genes) | ||
| klebsiella__cbst: MLST on the KpSC colibactin locus (clb genes) | ||
| klebsiella__rmpa2: typing for the rmpA2 gene | ||
| klebsiella__rmst: MLST on the KpSC Rmp locus (rmp genes) | ||
| klebsiella__smst: MLST on the KpSC salmochelin locus (iro genes) | ||
| klebsiella__ybst: MLST on the KpSC yersiniabactin locus (ybt and irp genes) | ||
| klebsiella_oxytoca_complex__mlst: chromosomal MLST for the Klebsiella oxytoca species complex | ||
| klebsiella_pneumo_complex__amr: Genotyping acquired genes and mutations for the Klebsiella pneumoniae species complex | ||
| klebsiella_pneumo_complex__kaptive: In silico serotyping of K and L locus for the Klebsiella pneumoniae species complex | ||
| klebsiella_pneumo_complex__mlst: chromosomal MLST for the Klebsiella pneumoniae species complex | ||
| klebsiella_pneumo_complex__resistance_class_count: Resistance gene classes count, excluding the Bla_chr class which is intrinsicresults of the | ||
| klebsiella_pneumo_complex__amr module | ||
| klebsiella_pneumo_complex__resistance_gene_count: Resistance genes counts, excluding the Bla class which is intrinsicresults of the | ||
| klebsiella_pneumo_complex__amr module | ||
| klebsiella_pneumo_complex__resistance_score: resistance score (0-3) for the Klebsiella pneumoniae species complex, based on the results of the | ||
| klebsiella_pneumo_complex__amr module | ||
| klebsiella_pneumo_complex__virulence_score: virulence score (0-5) for the Klebsiella pneumoniae species complex, based on the results of the abst, cbst | ||
| and ybst modules | ||
| klebsiella_pneumo_complex__wzi: WZI typing for K antigen prediction | ||
| ``` | ||
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| ## Example Usage | ||
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| ```bash | ||
| kleborate -a sample.fasta -o outdir -p preset | ||
| ``` |