adds stxtyper 1.0.27

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/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/sratoolkit)](https://hub.docker.com/r/staphb/sratoolkit) | <ul><li>2.9.2</li><li>[3.0.7](./sratoolkit/3.0.7/)</li></ul> | https://github.com/ncbi/sra-tools |
 | [SRST2](https://hub.docker.com/r/staphb/srst2/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/srst2)](https://hub.docker.com/r/staphb/srst2) | <ul><li>0.2.0</li><li>[0.2.0 + custom Vibrio cholerae database](srst2/0.2.0-vibrio-230224/README.md)</li></ul> | https://github.com/katholt/srst2 |
 | [Staramr](https://hub.docker.com/r/staphb/staramr/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/staramr)](https://hub.docker.com/r/staphb/staramr) | <ul><li>[0.5.1](./staramr/0.5.1/)</li><li>[0.7.1](./staramr/0.7.1/)</li><li>[0.8.0](./staramr/0.8.0/)</li><li>[0.10.0](./staramr/0.10.0/)</li></ul> | https://github.com/phac-nml/staramr |
-| [stxtyper](https://hub.docker.com/r/staphb/stxtyper) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/stxtyper)](https://hub.docker.com/r/staphb/stxtyper) | <ul><li>[1.0.24](stxtyper/1.0.24)</li></ul> | https://github.com/ncbi/stxtyper |
+| [stxtyper](https://hub.docker.com/r/staphb/stxtyper) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/stxtyper)](https://hub.docker.com/r/staphb/stxtyper) | <ul><li>[1.0.24](stxtyper/1.0.24/)</li><li>[1.0.27](stxtyper/1.0.27/)</li></ul> | https://github.com/ncbi/stxtyper |
 | [sylph](https://hub.docker.com/r/staphb/sylph) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/sylph)](https://hub.docker.com/r/staphb/sylph) | <ul><li>[0.4.1](./sylph/0.4.1)</li><li>[0.5.1](./sylph/0.5.1)</li><li>[0.6.0](./sylph/0.6.0)</li><li>[0.6.1](./sylph/0.6.1)</li></ul> | https://github.com/bluenote-1577/sylph |
 | [TBProfiler](https://hub.docker.com/r/staphb/tbprofiler/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/tbprofiler)](https://hub.docker.com/r/staphb/tbprofiler) | <ul><li>[4.3.0](./tbprofiler/4.3.0/)</li><li>[4.4.0](./tbprofiler/4.4.0/)</li><li>[4.4.2](./tbprofiler/4.4.2/)</li><li>[5.0.1](tbprofiler/5.0.1/)</li><li>[6.2.0](tbprofiler/6.2.0/)</li><li>[6.2.1](tbprofiler/6.2.1/)</li><li>[6.3.0](tbprofiler/6.3.0/)</li><li>[6.4.0](tbprofiler/6.4.0/)</li></ul> | https://github.com/jodyphelan/TBProfiler |
 | [TipToft](https://hub.docker.com/r/staphb/tiptoft/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/tiptoft)](https://hub.docker.com/r/staphb/tiptoft) | <ul><li>1.0.0</li><li>1.0.2</li></ul> | https://github.com/andrewjpage/tiptoft |

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="${STXTYPER_VER}"
+LABEL description="Search for Shiga toxin genes within bacterial genome assemblies"
+LABEL website="https://github.com/ncbi/stxtyper"
+LABEL license="https://github.com/ncbi/stxtyper/blob/main/LICENSE"
+LABEL maintainer="Curtis Kapsak"
+LABEL maintainer.email="[email protected]"
+
+# install dependencies via apt; cleanup apt garbage
+# blast from ubuntu:jammy is v2.12.0 (as of 2024-09-06)
+# procps is for ps command (required for nextflow)
+RUN apt-get update && apt-get install -y --no-install-recommends \
+ wget \
+ ca-certificates \
+ ncbi-blast+ \
+ procps && \
+ apt-get autoclean && rm -rf /var/lib/apt/lists/*
+
+# download pre-compiled binary
+RUN mkdir /stxtyper && \ 
+wget -q https://github.com/ncbi/stxtyper/releases/download/v${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'

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
+```