diff --git a/README.md b/README.md index 90ea43a87..38f6aedcf 100644 --- a/README.md +++ b/README.md @@ -191,7 +191,7 @@ To learn more about the docker pull rate limits and the open source software pro | [iVar](https://hub.docker.com/r/staphb/ivar/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/ivar)](https://hub.docker.com/r/staphb/ivar) | | https://github.com/andersen-lab/ivar | | [Jasmine](https://hub.docker.com/r/staphb/pbjasmine/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/pbjasmine)](https://hub.docker.com/r/staphb/pbjasmine) | | https://github.com/PacificBiosciences/jasmine | | [Kaptive](https://hub.docker.com/r/staphb/kaptive/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/kaptive)](https://hub.docker.com/r/staphb/kaptive) | | https://github.com/klebgenomics/Kaptive | -| [Kleborate](https://hub.docker.com/r/staphb/kleborate/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/kleborate)](https://hub.docker.com/r/staphb/kleborate) | | https://github.com/katholt/Kleborate/
https://github.com/katholt/Kaptive/ | +| [Kleborate](https://hub.docker.com/r/staphb/kleborate/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/kleborate)](https://hub.docker.com/r/staphb/kleborate) | | https://github.com/katholt/Kleborate/
https://github.com/katholt/Kaptive/ | | [kma](https://hub.docker.com/r/staphb/kma/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/kma)](https://hub.docker.com/r/staphb/kma) | | https://bitbucket.org/genomicepidemiology/kma/ | | [Kraken](https://hub.docker.com/r/staphb/kraken/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/kraken)](https://hub.docker.com/r/staphb/kraken) | | https://github.com/DerrickWood/kraken | | [Kraken2](https://hub.docker.com/r/staphb/kraken2/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/kraken2)](https://hub.docker.com/r/staphb/kraken2) | | https://github.com/DerrickWood/kraken2 | diff --git a/kleborate/3.1.2/Dockerfile b/kleborate/3.1.2/Dockerfile new file mode 100644 index 000000000..bb97c0119 --- /dev/null +++ b/kleborate/3.1.2/Dockerfile @@ -0,0 +1,66 @@ +FROM ubuntu:jammy as app + +# 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" + +LABEL base.image="ubuntu:jammy" +LABEL dockerfile.version="1" +LABEL software="Kleborate" +LABEL software.version="${KLEBORATE_VER}" +LABEL description="tool to screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC)" +LABEL website="https://github.com/katholt/Kleborate" +LABEL license="https://github.com/katholt/Kleborate/blob/master/LICENSE" +LABEL maintainer="Curtis Kapsak" +LABEL maintainer.email="kapsakcj@gmail.com" +LABEL maintainer2="Frank Ambrosio" +LABEL maintainer2.email="frank.ambrosio@theiagen.com" +LABEL maintainer3="Erin Young" +LABEL maintainer3.email="eriny@utah.gov" + +# install prerequisites. Cleanup apt garbage +RUN apt-get update && apt-get install -y --no-install-recommends \ + python3 \ + python3-pip \ + wget \ + ca-certificates \ + bzip2 \ + procps \ + curl && \ + rm -rf /var/lib/apt/lists/* && apt-get autoclean + +# mash; update UID and GID of mash files; make /data +# UID and GID changes because the original owner is UID: 1081147385 and GID: 1360859114 which does NOT play well with systems that limits GIDs and UIDs +RUN wget -q https://github.com/marbl/Mash/releases/download/v${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}/* + +# install minimap2 binary; make /data +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 + +# set PATH and TERM to avoid warnings +ENV PATH="/mash-Linux64-v${MASH_VER}:/minimap2-${MINIMAP2_VER}_x64-linux:${PATH}" + +# install kleborate +RUN pip install --no-cache-dir kleborate==${KLEBORATE_VER} && \ + mkdir /data + +# set working directory +WORKDIR /data + +CMD kleborate --help + +FROM app as test + +WORKDIR /test + +# 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 + +# print help and version info +RUN kleborate --help && kleborate --version && kleborate --list_modules \ No newline at end of file diff --git a/kleborate/3.1.2/README.md b/kleborate/3.1.2/README.md new file mode 100644 index 000000000..2765be3f6 --- /dev/null +++ b/kleborate/3.1.2/README.md @@ -0,0 +1,79 @@ +# Kleborate container + +Main tool : [Kleborate](https://github.com/katholt/Kleborate) + +Additional tools: + +- [mash](https://github.com/marbl/Mash) version 2.3 +- [minimap2]() version 2.28 + +Full documentation: [https://github.com/katholt/Kleborate/wiki](https://github.com/katholt/Kleborate/wiki) + +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 + +Kleborate has models for both Klebsiella and Escherichia species. The available presets and models are listed below. + +Available presets: kpsc, kosc, escherichia + +``` +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 +``` + + +## Example Usage + +```bash +kleborate -a sample.fasta -o outdir -p preset +```