diff --git a/README.md b/README.md index 8849f529d..63d16d473 100644 --- a/README.md +++ b/README.md @@ -296,7 +296,7 @@ To learn more about the docker pull rate limits and the open source software pro | [SRA-toolkit](https://hub.docker.com/r/staphb/sratoolkit/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/sratoolkit)](https://hub.docker.com/r/staphb/sratoolkit) | | https://github.com/ncbi/sra-tools | | [SRST2](https://hub.docker.com/r/staphb/srst2/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/srst2)](https://hub.docker.com/r/staphb/srst2) | | https://github.com/katholt/srst2 | | [Staramr](https://hub.docker.com/r/staphb/staramr/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/staramr)](https://hub.docker.com/r/staphb/staramr) | | https://github.com/phac-nml/staramr | -| [stxtyper](https://hub.docker.com/r/staphb/stxtyper)
[![docker pulls](https://badgen.net/docker/pulls/staphb/stxtyper)](https://hub.docker.com/r/staphb/stxtyper) | | https://github.com/ncbi/stxtyper | +| [stxtyper](https://hub.docker.com/r/staphb/stxtyper)
[![docker pulls](https://badgen.net/docker/pulls/staphb/stxtyper)](https://hub.docker.com/r/staphb/stxtyper) | | https://github.com/ncbi/stxtyper | | [sylph](https://hub.docker.com/r/staphb/sylph)
[![docker pulls](https://badgen.net/docker/pulls/staphb/sylph)](https://hub.docker.com/r/staphb/sylph) | | https://github.com/bluenote-1577/sylph | | [TBProfiler](https://hub.docker.com/r/staphb/tbprofiler/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/tbprofiler)](https://hub.docker.com/r/staphb/tbprofiler) | | https://github.com/jodyphelan/TBProfiler | | [TipToft](https://hub.docker.com/r/staphb/tiptoft/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/tiptoft)](https://hub.docker.com/r/staphb/tiptoft) | | https://github.com/andrewjpage/tiptoft | diff --git a/stxtyper/1.0.27/Dockerfile b/stxtyper/1.0.27/Dockerfile new file mode 100644 index 000000000..680dbae12 --- /dev/null +++ b/stxtyper/1.0.27/Dockerfile @@ -0,0 +1,55 @@ +FROM ubuntu:jammy AS app + +ARG STXTYPER_VER="1.0.27" + +LABEL base.image="ubuntu:jammy" +LABEL dockerfile.version="1" +LABEL software="stxtyper" +LABEL software.version="${STXTYPER_VER}" +LABEL description="Search for Shiga toxin genes within bacterial genome assemblies" +LABEL website="https://github.com/ncbi/stxtyper" +LABEL license="https://github.com/ncbi/stxtyper/blob/main/LICENSE" +LABEL maintainer="Curtis Kapsak" +LABEL maintainer.email="kapsakcj@gmail.com" + +# install dependencies via apt; cleanup apt garbage +# blast from ubuntu:jammy is v2.12.0 (as of 2024-09-06) +# procps is for ps command (required for nextflow) +RUN apt-get update && apt-get install -y --no-install-recommends \ + wget \ + ca-certificates \ + ncbi-blast+ \ + procps && \ + apt-get autoclean && rm -rf /var/lib/apt/lists/* + +# download pre-compiled binary +RUN mkdir /stxtyper && \ +wget -q https://github.com/ncbi/stxtyper/releases/download/v${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${STXTYPER_VER}_x86_64_Linux.tar.gz && \ +ls -lh /stxtyper + +# set PATH to include where stxtyper & fasta_check executables exist +ENV PATH="${PATH}:/stxtyper" \ +TERM=xterm-256color + +# set final working directory as /data for passing data in/out of container +WORKDIR /data + +FROM app AS test + +# print version and help options & run the supplied tests +RUN tblastn -version && \ +stxtyper --version && \ +stxtyper --help && \ +cd /stxtyper && \ +bash test_stxtyper.sh + +# 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' diff --git a/stxtyper/1.0.27/README.md b/stxtyper/1.0.27/README.md new file mode 100644 index 000000000..16e21e054 --- /dev/null +++ b/stxtyper/1.0.27/README.md @@ -0,0 +1,29 @@ +# stxtyper container + +Main tool: [stxtyper](https://github.com/ncbi/stxtyper) + +Additional tools: + +- ncbi-blast+ 2.12.0 + +Basic information on how to use this tool: + +- executable: `stxtyper` +- help: `stxtyper --help` +- version: `stxtyper --version` +- description: Detects and types Shiga toxin genes in nucleotide sequences + +Full documentation: [https://github.com/ncbi/stxtyper](https://github.com/ncbi/stxtyper) + +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. + +## Example Usage + +```bash +# stxtyper accepts both gzipped and uncompressed FASTA files +stxtyper -n GCA_012224845.2_ASM1222484v2_genomic.fna.gz -o stxtyper-results.tsv + +$ 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 +```