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adding staramr version 0.11.1 (#1472)
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‎.github/workflows/update_staramr.yml‎

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##### ------------------------------------------------------------------------------------------------ #####
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##### This caller workflow tests, builds, and pushes the image to Docker Hub and Quay using the most #####
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##### recent databases. #####
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##### It takes no manual input. #####
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##### ------------------------------------------------------------------------------------------------ #####
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name: Update STARAMR
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on:
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workflow_dispatch:
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schedule:
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- cron: '30 7 1 1,7 *'
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# Runs at 07:30 on the 1st day of January and July
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run-name: Updating STARAMR
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jobs:
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update:
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if: github.repository == 'StaPH-B/docker-builds'
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runs-on: ubuntu-latest
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steps:
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- name: pull repo
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uses: actions/checkout@v4
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- name: set version
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id: latest_version
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run: |
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version=0.11.1
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echo "version=$version" >> $GITHUB_OUTPUT
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file=build-files/staramr/$version/Dockerfile
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ls $file
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echo "file=$file" >> $GITHUB_OUTPUT
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- name: set up docker buildx
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id: buildx
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uses: docker/setup-buildx-action@v3
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- name: build to test
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id: docker_build_to_test
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uses: docker/build-push-action@v5
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with:
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file: ${{ steps.latest_version.outputs.file }}
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target: test
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load: true
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push: false
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tags: staramr:update
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- name: Get current date
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id: date
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run: |
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date=$(date '+%Y-%m-%d')
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echo "the date is $date"
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echo "date=$date" >> $GITHUB_OUTPUT
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- name: Login to DockerHub
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uses: docker/login-action@v3
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with:
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username: ${{ secrets.DOCKER_HUB_USERNAME }}
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password: ${{ secrets.DOCKER_HUB_ACCESS_TOKEN }}
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- name: Login to Quay
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uses: docker/login-action@v3
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with:
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registry: quay.io
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username: ${{ secrets.QUAY_USERNAME }}
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password: ${{ secrets.QUAY_ROBOT_TOKEN }}
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- name: Build and push user-defined tag to DockerHub
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id: docker_build_user_defined_tag
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uses: docker/build-push-action@v5
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with:
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file: ${{ steps.latest_version.outputs.file }}
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target: app
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push: true
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tags: |
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staphb/staramr:${{ steps.latest_version.outputs.version }}-${{ steps.date.outputs.date }}
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staphb/staramr:latest
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quay.io/staphb/staramr:${{ steps.latest_version.outputs.version }}-${{ steps.date.outputs.date }}
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quay.io/staphb/staramr:latest

‎README.md‎

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@@ -323,7 +323,7 @@ To learn more about the docker pull rate limits and the open source software pro
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| [SPAdes](https://hub.docker.com/r/staphb/spades/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/spades)](https://hub.docker.com/r/staphb/spades) | <details><summary>Click to see all versions</summary> <ul><li>[3.8.2](./build-files/spades/3.8.2/)</li><li>[3.12.0](./build-files/spades/3.12.0/)</li><li>[3.13.0](./build-files/spades/3.13.0/)</li><li>[3.14.0](./build-files/spades/3.14.0/)</li><li>[3.14.1](./build-files/spades/3.14.1/)</li><li>[3.15.0](./build-files/spades/3.15.0/)</li><li>[3.15.1](./build-files/spades/3.15.1/)</li><li>[3.15.2](./build-files/spades/3.15.2/)</li><li>[3.15.3](./build-files/spades/3.15.3/)</li><li>[3.15.4](./build-files/spades/3.15.4/)</li><li>[3.15.5](./build-files/spades/3.15.5/)</li><li>[4.0.0](./build-files/spades/4.0.0/)</li><li>[4.1.0](./build-files/spades/4.1.0/)</li><li>[4.2.0](./build-files/spades/4.2.0/)</li></ul></details> | https://github.com/ablab/spades </br> http://cab.spbu.ru/software/spades/ |
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| [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) | <details><summary>Click to see all versions</summary> <ul><li>[2.9.2](./build-files/sratoolkit/2.9.2/)</li><li>[3.0.7](./build-files/sratoolkit/3.0.7/)</li><li>[3.2.0](./build-files/sratoolkit/3.2.0/)</li><li>[3.2.1](./build-files/sratoolkit/3.2.1/)</li></ul> </details> | https://github.com/ncbi/sra-tools |
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| [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) | <details><summary>Click to see all versions</summary> <ul><li>[0.2.0](./build-files/srst2/0.2.0/)</li><li>[0.2.0 + custom Vibrio cholerae database](./build-files/srst2/0.2.0-vibrio-230224/README.md)</li></ul> </details> | https://github.com/katholt/srst2 |
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| [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) | <details><summary>Click to see all versions</summary> <ul><li>[0.5.1](./build-files/staramr/0.5.1/)</li><li>[0.7.1](./build-files/staramr/0.7.1/)</li><li>[0.8.0](./build-files/staramr/0.8.0/)</li><li>[0.10.0](./build-files/staramr/0.10.0/)</li><li>[0.11.0](./build-files/staramr/0.11.0/)</li></ul> </details> | https://github.com/phac-nml/staramr |
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| [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) | <details><summary>Click to see all versions</summary> <ul><li>[0.5.1](./build-files/staramr/0.5.1/)</li><li>[0.7.1](./build-files/staramr/0.7.1/)</li><li>[0.8.0](./build-files/staramr/0.8.0/)</li><li>[0.10.0](./build-files/staramr/0.10.0/)</li><li>[0.11.0](./build-files/staramr/0.11.0/)</li><li>[0.11.1](./build-files/staramr/0.11.1/)</li></ul> </details> | https://github.com/phac-nml/staramr |
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| [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) | <details><summary>Click to see all versions</summary> <ul><li>[1.0.24](./build-files/stxtyper/1.0.24/)</li><li>[1.0.27](./build-files/stxtyper/1.0.27/)</li><li>[1.0.31](./build-files/stxtyper/1.0.31/)</li><li>[1.0.40](./build-files/stxtyper/1.0.40/)</li><li>[1.0.42](./build-files/stxtyper/1.0.42/)</li></ul> </details> | https://github.com/ncbi/stxtyper |
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| [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) | <details><summary>Click to see all versions</summary> <ul><li>[0.4.1](./build-files/sylph/0.4.1)</li><li>[0.5.1](./build-files/sylph/0.5.1)</li><li>[0.6.0](./build-files/sylph/0.6.0/)</li><li>[0.6.1](./build-files/sylph/0.6.1)</li><li>[0.8.0](./build-files/sylph/0.8.0)</li><li>[0.8.1](./build-files/sylph/0.8.1/)</li><li>[0.9.0](./build-files/sylph/0.9.0/)</li></ul> </details> | https://github.com/bluenote-1577/sylph |
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| [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) | <details><summary>Click to see all versions</summary> <ul><li>[4.3.0](./build-files/tbprofiler/4.3.0/)</li><li>[4.4.0](./build-files/tbprofiler/4.4.0/)</li><li>[4.4.2](./build-files/tbprofiler/4.4.2/)</li><li>[5.0.1](./build-files/tbprofiler/5.0.1/)</li><li>[6.2.0](./build-files/tbprofiler/6.2.0/)</li><li>[6.2.1](./build-files/tbprofiler/6.2.1/)</li><li>[6.3.0](./build-files/tbprofiler/6.3.0/)</li><li>[6.4.0](./build-files/tbprofiler/6.4.0/)</li><li>[6.4.1](./build-files/tbprofiler/6.4.1/)</li><li>[6.6.2](./build-files/tbprofiler/6.6.2/)</li><li>[6.6.3](./build-files/tbprofiler/6.6.3/)</li><li>[6.6.5](./build-files/tbprofiler/6.6.5/)</li></ul> </details> | https://github.com/jodyphelan/TBProfiler <br/> https://github.com/jodyphelan/tbdb |

‎build-files/staramr/0.11.1/Dockerfile‎

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# base image
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FROM python:3.9-slim AS app
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ARG STARAMR_VER="0.11.1"
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ARG MLST_VER="2.23.0"
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ARG ANY2FASTA_VERSION="0.4.2"
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LABEL base.image="python:3.9-slim"
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LABEL dockerfile.version="1"
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LABEL software="staramr"
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LABEL software.version="${STARAMR_VER}"
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LABEL description="staramr scans bacterial genome contigs for AMR genes and plasmids"
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LABEL website="https://github.com/phac-nml/staramr"
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LABEL license="https://github.com/phac-nml/staramr/blob/master/LICENSE"
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LABEL maintainer="Rachael St. Jacques"
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LABEL maintainer.email="rachael.stjacques@dgs.virginia.gov"
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LABEL maintainer2="Curtis Kapsak"
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LABEL maintainer2.email="curtis.kapsak@theiagen.com"
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# install dependencies via apt; cleanup apt garbage
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# ncbi-blast+ is v2.9.0 in ubuntu:focal (as of August 2022)
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RUN apt-get update && apt-get install -y --no-install-recommends \
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git \
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wget \
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libmoo-perl \
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liblist-moreutils-perl \
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libjson-perl \
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gzip \
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file \
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ncbi-blast+ \
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procps \
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ca-certificates && \
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apt-get autoclean && rm -rf /var/lib/apt/lists/*
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# any2fasta
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RUN wget -q https://github.com/tseemann/any2fasta/archive/refs/tags/v${ANY2FASTA_VERSION}.tar.gz && \
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tar -xvf v${ANY2FASTA_VERSION}.tar.gz && \
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rm v${ANY2FASTA_VERSION}.tar.gz && \
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cd any2fasta-${ANY2FASTA_VERSION} && \
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chmod +x any2fasta
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# mlst
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# apt dependencies: wget libmoo-perl liblist-moreutils-perl libjson-perl gzip file
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# also requires blast 2.9.0 or greater
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RUN wget -q https://github.com/tseemann/mlst/archive/v${MLST_VER}.tar.gz && \
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tar -xzf v${MLST_VER}.tar.gz && \
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rm v${MLST_VER}.tar.gz
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# staramr; make /data
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RUN wget -q https://github.com/phac-nml/staramr/archive/refs/tags/${STARAMR_VER}.tar.gz && \
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pip install ${STARAMR_VER}.tar.gz --no-cache-dir && \
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rm -rf ${STARAMR_VER}.tar.gz && \
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mkdir /data
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# set $PATH and locale settings for singularity
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ENV PATH="${PATH}:/mlst-${MLST_VER}/bin:/any2fasta-${ANY2FASTA_VERSION}/" \
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LC_ALL=C
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# update staramr default databases and print db info
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RUN staramr db update -d && staramr db info
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CMD ["staramr", "--help"]
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WORKDIR /data
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FROM app AS test
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RUN staramr --help && staramr --version
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# download the FASTA file for ${GENBANK_ACCESSION}
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# Salmonella Enterica isolate from PHE-UK: https://www.ncbi.nlm.nih.gov/assembly/GCA_010941835.1/
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RUN wget -q https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/010/941/835/GCA_010941835.1_PDT000052640.3/GCA_010941835.1_PDT000052640.3_genomic.fna.gz && \
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gzip -d GCA_010941835.1_PDT000052640.3_genomic.fna.gz
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# run staramr on the second genome mentioned on staramr's documentation; print resulting TSVs
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RUN staramr search -o /data/staramr-test-Salmonella \
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--pointfinder-organism salmonella \
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--plasmidfinder-database-type enterobacteriales \
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/data/GCA_010941835.1_PDT000052640.3_genomic.fna
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# installing bsdmainutils for installing "column" command
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RUN apt-get update && apt-get install -y --no-install-recommends bsdmainutils
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# neatly print out resulting/output TSVs
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RUN column -t /data/staramr-test-Salmonella/mlst.tsv && echo && \
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column -t /data/staramr-test-Salmonella/pointfinder.tsv && echo && \
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column -t /data/staramr-test-Salmonella/plasmidfinder.tsv && echo && \
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column -t /data/staramr-test-Salmonella/resfinder.tsv && echo && \
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column -t /data/staramr-test-Salmonella/detailed_summary.tsv && echo && \
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column -t /data/staramr-test-Salmonella/summary.tsv
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RUN staramr db info

‎build-files/staramr/0.11.1/README.md‎

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# staramr container
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Main tool : [staramr](https://github.com/phac-nml/staramr)
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Additional tools:
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- mlst 2.23.0
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- ncbi-blast+ 2.12.0+
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- any2fasta 0.4.2
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- Databases for PlasmidFinder, PointFinder, ResFinder
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Database version information:
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```
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##### staramr db information at time of docker image build #####
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resfinder_db_dir = /usr/local/lib/python3.9/site-packages/staramr/databases/data/update/resfinder
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resfinder_db_url = https://bitbucket.org/genomicepidemiology/resfinder_db.git
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resfinder_db_commit = c0aa05c5cae9da75e4395e9fa3dd5057e3bf4a75
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resfinder_db_date = Tue, 09 Sep 2025 18:35
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pointfinder_db_dir = /usr/local/lib/python3.9/site-packages/staramr/databases/data/update/pointfinder
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pointfinder_db_url = https://bitbucket.org/genomicepidemiology/pointfinder_db.git
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pointfinder_db_commit = 29d83a51cb41e429e38e46b1096608b9accb2b2a
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pointfinder_db_date = Fri, 22 Aug 2025 09:34
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pointfinder_organisms_all = campylobacter, enterococcus_faecalis, enterococcus_faecium, escherichia_coli, helicobacter_pylori, klebsiella, mycobacterium_tuberculosis, neisseria_gonorrhoeae, plasmodium_falciparum, salmonella, staphylococcus_aureus
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pointfinder_organisms_valid = campylobacter, enterococcus_faecalis, enterococcus_faecium, escherichia_coli, helicobacter_pylori, salmonella
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plasmidfinder_db_dir = /usr/local/lib/python3.9/site-packages/staramr/databases/data/update/plasmidfinder
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plasmidfinder_db_url = https://bitbucket.org/genomicepidemiology/plasmidfinder_db.git
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plasmidfinder_db_commit = 49c24c1c9401fa175fbcfdbd4b37227a160baca4
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plasmidfinder_db_date = Wed, 10 Sep 2025 18:56
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mlst_version = 2.23.0
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pointfinder_gene_drug_version = 070623
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resfinder_gene_drug_version = 072423
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```
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STARAMR uses several databases that it does not maintain. As such, this image is re-built twice a year for the latest of these databases {latest-version}={date of rebuilding}.
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Full documentation: https://github.com/phac-nml/staramr
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staramr scans bacterial genome contigs for AMR genes and plasmids
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## Example Usage
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```bash
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# run "staramr search" on a genome assembly (broken into multiple lines for readability)
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staramr search -o /data/staramrtest-Salmonella \
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--pointfinder-organism salmonella \
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--plasmidfinder-database-type enterobacteriales \
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/data/salmonella_enterica_assembly.fasta
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# to get database information
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staramr db info
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```

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