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‎.github/workflows/update-plassembler.yml‎

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- name: set version
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id: latest_version
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run: |
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version=1.8.1
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version=1.8.2
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echo "version=$version" >> $GITHUB_OUTPUT
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file=build-files/plassembler/$version/Dockerfile
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staphb/plassembler:${{ steps.latest_version.outputs.version }}-${{ steps.date.outputs.date }}
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staphb/plassembler:latest
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quay.io/staphb/plassembler:${{ steps.latest_version.outputs.version }}-${{ steps.date.outputs.date }}
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quay.io/staphb/plassembler:latest
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quay.io/staphb/plassembler:latest

‎Program_Licenses.md‎

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| geNomad | ACADEMIC, INTERNAL, RESEARCH & DEVELOPMENT, NON-COMMERCIAL USE ONLY | https://github.com/apcamargo/genomad/blob/main/LICENSE |
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| GenoVi | BY-NC-SA Creative Commons License | https://github.com/robotoD/GenoVi/blob/main/LICENSE.txt |
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| gfastats | MIT | https://github.com/vgl-hub/gfastats/blob/main/LICENSE |
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| gotree | GPL-2.0 license | https://github.com/evolbioinfo/gotree/blob/master/LICENSE |
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| Grandeur | GNU General Public License v3.0 | https://github.com/UPHL-BioNGS/Grandeur/blob/main/LICENSE |
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| Gubbins | GNU GPLv2 | https://github.com/nickjcroucher/gubbins/blob/master/LICENSE |
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| HeatCluster | GPL-3.0 | https://github.com/DrB-S/heatcluster/blob/main/LICENSE |
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| HeatCluster | GPL-3.0 | https://github.com/DrB-S/heatcluster/blob/main/LICENSE ; https://github.com/erinyoung/heatcluster/blob/main/LICENSE |
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| Hmmer | BSD-3 | http://eddylab.org/software/hmmer/Userguide.pdf |
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| HoCoRT | MIT | https://github.com/ignasrum/hocort?tab=MIT-1-ov-file#readme |
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| homopolish | GNU GPLv3 | https://github.com/ythuang0522/homopolish/blob/master/LICENSE |

‎README.md‎

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‎build-files/arborview/0.1.3/Dockerfile‎

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FROM ubuntu:noble AS app
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ARG ARG ARBORVIEW_VER="0.1.3"
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LABEL base.image="ubuntu:noble"
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LABEL dockerfile.version="1"
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LABEL software="ArborView"
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LABEL software.version="${ARBORVIEW_VER}"
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LABEL description="Visualize phylogenetic trees with associated sample metadata"
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LABEL website="https://github.com/phac-nml/ArborView"
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LABEL license="https://github.com/phac-nml/ArborView/tree/main?tab=readme-ov-file#legal-and-compliance-information"
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LABEL maintainer="Kutluhan Incekara"
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LABEL maintainer.email="kutluhan.incekara@ct.gov"
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RUN apt-get update && apt-get install -y --no-install-recommends \
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wget \
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python-is-python3 && \
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apt-get autoclean && rm -rf /var/lib/apt/lists/*
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RUN wget --no-check-certificate https://github.com/phac-nml/ArborView/archive/refs/tags/v${ARBORVIEW_VER}.tar.gz && \
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tar -xvf v${ARBORVIEW_VER}.tar.gz && rm v${ARBORVIEW_VER}.tar.gz &&\
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chmod +x /ArborView-${ARBORVIEW_VER}/scripts/inline_arborview.py
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ENV PATH="/ArborView-${ARBORVIEW_VER}/scripts/:$PATH" \
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LC_ALL=C
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CMD [ "inline_arborview.py", "--help" ]
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WORKDIR /data
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## Test ##
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FROM app AS test
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RUN inline_arborview.py --help
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RUN inline_arborview.py -d /ArborView-${ARBORVIEW_VER}/example/ultrametric_simple_tree_metadata.tsv -n /ArborView-${ARBORVIEW_VER}/example/ultrametric_simple_tree.nwk -o test.html

‎build-files/arborview/0.1.3/README.md‎

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# ArborView container
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Main tool: [ArborView](https://github.com/phac-nml/ArborView)
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Code repository: https://github.com/phac-nml/ArborView
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Additional tools:
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Basic information on how to use this tool:
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- executable: inline_arborview.py
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- help: `-h`, `--help`
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- version:
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- description: ArborView visualize newick trees with associated sample metadata. `inline_arborview.py` embeds the newick file and tabular data directly into the html file eliminating the need for user data upload.
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Additional information:
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- Web server: https://phac-nml.github.io/ArborView/main/index.html
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- metadata format
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| sample_id | serovar | mlst_st | earliest_date | state_province | source_type | source_site | age | sex | reported_id | national_outbreak_code |
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| :--- | :--- | :--- | :--- | :--- | :--- | :--- | :--- | :--- | :--- | :--- |
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| S1 | Enteritidis | 11.0 | 2021-06-19 | ON | Human | Stool | 20 | F | Salmonella | None |
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| S2 | Enteritidis | 11.0 | 2006-01-03 | QC | Animal | Chicken | 52 | M | Salmonella | None |
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Full documentation: https://github.com/phac-nml/ArborView
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## Example Usage
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```bash
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inline_arborview.py -d metadata.tsv -n tree.nwk -o output.html
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```

‎build-files/augur/33.0.0/Dockerfile‎

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FROM python:3.11-slim AS app
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ARG AUGUR_VER="33.0.0"
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ARG SEQKIT_VER="2.12.0"
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# LABEL instructions tag the image with metadata that might be important to the user
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# Optional, but highly recommended
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LABEL base.image="python:3.11-slim"
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LABEL dockerfile.version="1"
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LABEL software="augur"
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LABEL software.version=${AUGUR_VER}
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LABEL description="Augur is the bioinformatics toolkit we use to track evolution from sequence and serological data.The output of augur is a series of JSONs that can be used to visualize your results using Auspice."
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LABEL website="https://github.com/nextstrain/augur"
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LABEL license="https://github.com/nextstrain/augur/blob/master/LICENSE.txt"
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LABEL maintainer="John Arnn"
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LABEL maintainer.email="jarnn@utah.gov"
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# 'RUN' executes code during the build
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# Install dependencies via apt-get or yum if using a centos or fedora base
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RUN apt-get update && apt-get install -y --no-install-recommends \
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procps \
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ca-certificates \
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wget \
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mafft \
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iqtree \
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raxml \
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fasttree \
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vcftools && \
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apt-get autoclean && rm -rf /var/lib/apt/lists/*
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# install seqkit
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RUN wget -q https://github.com/shenwei356/seqkit/releases/download/v${SEQKIT_VER}/seqkit_linux_amd64.tar.gz && \
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tar -xzf seqkit_linux_amd64.tar.gz && \
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mv seqkit /usr/local/bin/. && \
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rm seqkit_linux_amd64.tar.gz
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# install augur
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RUN wget -q https://github.com/nextstrain/augur/archive/refs/tags/${AUGUR_VER}.tar.gz && \
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tar -xzf ${AUGUR_VER}.tar.gz && \
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pip install ${AUGUR_VER}.tar.gz --no-cache-dir && \
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rm -v ${AUGUR_VER}.tar.gz
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# augur tree calls iqtree
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RUN ln -s /usr/bin/iqtree2 /usr/bin/iqtree
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CMD [ "augur", "--help" ]
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WORKDIR /data
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FROM app AS test
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RUN augur --help
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WORKDIR /test
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RUN apt-get update && apt-get install -y --no-install-recommends git
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RUN git clone https://github.com/nextstrain/zika-tutorial && \
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cd zika-tutorial && \
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mkdir results && \
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augur index \
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--sequences data/sequences.fasta \
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--output results/sequence_index.tsv && \
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augur filter \
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--sequences data/sequences.fasta \
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--sequence-index results/sequence_index.tsv \
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--metadata data/metadata.tsv \
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--exclude config/dropped_strains.txt \
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--output-sequences results/filtered.fasta \
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--group-by country year month \
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--sequences-per-group 20 \
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--min-date 2012 && \
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augur align \
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--sequences results/filtered.fasta \
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--reference-sequence config/zika_outgroup.gb \
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--output results/aligned.fasta \
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--fill-gaps && \
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augur tree \
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--alignment results/aligned.fasta \
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--output results/tree_raw.nwk && \
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augur refine \
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--tree results/tree_raw.nwk \
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--alignment results/aligned.fasta \
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--metadata data/metadata.tsv \
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--output-tree results/tree.nwk \
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--output-node-data results/branch_lengths.json \
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--timetree \
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--coalescent opt \
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--date-confidence \
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--date-inference marginal \
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--clock-filter-iqd 4 && \
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augur traits \
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--tree results/tree.nwk \
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--metadata data/metadata.tsv \
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--output-node-data results/traits.json \
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--columns region country \
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--confidence && \
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augur ancestral \
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--tree results/tree.nwk \
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--alignment results/aligned.fasta \
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--output-node-data results/nt_muts.json \
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--inference joint && \
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augur translate \
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--tree results/tree.nwk \
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--ancestral-sequences results/nt_muts.json \
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--reference-sequence config/zika_outgroup.gb \
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--output-node-data results/aa_muts.json && \
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augur export v2 \
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--tree results/tree.nwk \
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--metadata data/metadata.tsv \
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--node-data results/branch_lengths.json \
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results/traits.json \
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results/nt_muts.json \
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results/aa_muts.json \
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--colors config/colors.tsv \
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--lat-longs config/lat_longs.tsv \
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--auspice-config config/auspice_config.json \
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--output auspice/zika.json && \
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head auspice/zika.json
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RUN pip list

‎build-files/augur/33.0.0/README.md‎

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# Augur Container
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Main tool: [Augur](https://github.com/nextstrain/augur)
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Definition: One held to foretell events by omens.
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Augur is the bioinformatics toolkit we use to track evolution from sequence and serological data. It provides a collection of commands which are designed to be composable into larger processing pipelines.
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The output of augur is a series of JSONs that can be used to visualize your results using Auspice.
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Note: Auspice is a different tool.
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## Additional dependencies
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- fasttree 2.1.11-2
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- python 3.11.13
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- iqtree 2.0.7+dfsg-1+b2
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- mafft 7.505-1
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- raxml 8.2.13+dfsg-2+b1
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- vcftools 0.1.16-3+b1
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- seqkit 2.12.0
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<details>
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<summary>Additional tools installed via pip:</summary>
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```
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Package Version
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------------------------- -----------
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attrs 25.4.0
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bcbio-gff 0.7.1
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biopython 1.86
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contourpy 1.3.3
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cvxopt 1.3.3
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cycler 0.12.1
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fonttools 4.61.1
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isal 1.8.0
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isodate 0.7.2
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jsonschema 4.26.0
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jsonschema-specifications 2025.9.1
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kiwisolver 1.4.9
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matplotlib 3.10.8
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networkx 3.6.1
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nextstrain-augur 33.0.0
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numpy 2.4.2
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packaging 26.0
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pandas 2.3.3
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phylo-treetime 0.11.4
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pillow 12.1.1
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pip 24.0
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pyfastx 2.3.0
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pyparsing 3.3.2
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python-calamine 0.6.1
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python-dateutil 2.9.0.post0
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pytz 2025.2
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PyYAML 6.0.3
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referencing 0.37.0
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rpds-py 0.30.0
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scipy 1.17.0
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setuptools 79.0.1
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six 1.17.0
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typing_extensions 4.15.0
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tzdata 2025.3
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wheel 0.45.1
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xopen 2.0.2
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zlib-ng 1.0.0
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zstandard 0.25.0
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```
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</details>
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## Example Usage
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```bash
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augur index --sequences sequences.fasta --output sequence_index.tsv
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```
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```bash
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augur filter \
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--sequences data/sequences.fasta \
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--sequence-index results/sequence_index.tsv \
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--metadata data/metadata.tsv \
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--exclude config/dropped_strains.txt \
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--output-sequences results/filtered.fasta \
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--group-by country year month \
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--sequences-per-group 20 \
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--min-date 2012
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```
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Better documentation can be found [here.](https://docs.nextstrain.org/en/latest/tutorials/creating-a-workflow.html)

‎build-files/bakta/1.12.0/Dockerfile‎

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FROM mambaorg/micromamba:2.5.0-ubuntu22.04 AS app
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ARG BAKTA_VER="1.12.0"
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# 'LABEL' instructions tag the image with metadata that might be important to the user
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LABEL base.image="mambaorg/micromamba:2.5.0-ubuntu22.04"
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LABEL dockerfile.version="1"
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LABEL software="Bakta"
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LABEL software.version="${BAKTA_VER}"
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LABEL description="rapid & standardized annotation of bacterial genomes, MAGs & plasmids"
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LABEL website="https://github.com/oschwengers/bakta"
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LABEL license="https://github.com/oschwengers/bakta/blob/main/LICENSE"
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LABEL maintainer="Erin Young"
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LABEL maintainer.email="eriny@utah.gov"
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USER root
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RUN apt-get update && apt-get install -y --no-install-recommends \
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wget \
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ca-certificates && \
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apt-get autoclean && rm -rf /var/lib/apt/lists/*
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RUN micromamba install --name base -c conda-forge -c bioconda bakta=${BAKTA_VER} && \
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micromamba clean -a -f -y && \
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mkdir /data
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ENV PATH="/opt/conda/bin/:$PATH" \
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LC_ALL=C
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CMD ["bakta", "--help"]
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WORKDIR /data
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FROM app AS test
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WORKDIR /test
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RUN bakta --help && \
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bakta_db --help && \
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bakta --version
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RUN bakta_db list && \
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bakta_db download --type light
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RUN wget -q https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/195/815/GCF_000195815.1_ASM19581v1/GCF_000195815.1_ASM19581v1_genomic.fna.gz && \
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gunzip GCF_000195815.1_ASM19581v1_genomic.fna.gz && \
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bakta --db /test/db-light GCF_000195815.1_ASM19581v1_genomic.fna && \
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head GCF_000195815.1_ASM19581v1_genomic.gbff
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RUN micromamba list

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