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erinyoung merged 1 commit into from
Jun 26, 2026
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Augur 33.4.1 #1721

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2 changes: 1 addition & 1 deletion README.md
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Expand Up @@ -121,7 +121,7 @@ To learn more about the docker pull rate limits and the open source software pro
| [artic-ncov2019-nanopolish](https://hub.docker.com/r/staphb/artic-ncov2019-nanopolish) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/artic-ncov2019-nanopolish)](https://hub.docker.com/r/staphb/artic-ncov2019-nanopolish) | <details><summary>Click to see all versions</summary> <ul><li>[1.1.0](./build-files/artic-ncov2019-nanopolish/1.1.0/)</ul> </details> | https://github.com/artic-network/artic-ncov2019 |
| [artic-tools](https://hub.docker.com/r/staphb/artic-tools) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/artic-tools)](https://hub.docker.com/r/staphb/artic-tools) | <details><summary> Click to see all versions</summary> <ul><li>[0.3.1](./build-files/artic-tools/0.3.1/)</ul></details> | https://github.com/will-rowe/artic-tools
| [assembly_snptyper](https://hub.docker.com/r/staphb/assembly_snptyperh) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/assembly_snptyper)](https://hub.docker.com/r/staphb/assembly_snptyper) | <details><summary>Click to see all versions</summary> <ul><li>[0.1.1](./build-files/assembly_snptyper/0.1.1/)</li></ul> </details> | https://github.com/boasvdp/assembly_snptyper |
| [Augur](https://hub.docker.com/r/staphb/augur) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/augur)](https://hub.docker.com/r/staphb/augur) | <details><summary>Click to see all versions</summary> <ul><li>[6.3.0](./build-files/augur/6.3.0/)</li><li>[7.0.2](./build-files/augur/7.0.2/)</li><li>[8.0.0](./build-files/augur/8.0.0/)</li><li>[9.0.0](./build-files/augur/9.0.0/)</li><li>[16.0.3](./build-files/augur/16.0.3/)</li><li>[24.2.2](./build-files/augur/24.2.2/)</li><li>[24.2.3](./build-files/augur/24.2.3/)</li><li>[24.3.0](./build-files/augur/24.3.0/)</li><li>[24.4.0](./build-files/augur/24.4.0/)</li><li>[26.0.0](./build-files/augur/26.0.0/)</li><li>[27.0.0](./build-files/augur/27.0.0/)</li><li>[28.0.1](./build-files/augur/28.0.1/)</li><li>[29.0.0](./build-files/augur/29.0.0/)</li><li>[30.0.0](./build-files/augur/30.0.0/)</li><li>[31.1.0](./build-files/augur/31.1.0/)</li><li>[31.3.0](./build-files/augur/31.3.0/)</li><li>[31.4.0](./build-files/augur/31.4.0/)</li><li>[31.5.0](./build-files/augur/31.5.0/)</li><li>[32.0.0](./build-files/augur/32.0.0/)</li><li>[32.1.0](./build-files/augur/32.1.0/)</li><li>[33.0.0](./build-files/augur/33.0.0/)</li><li>[33.0.1](./build-files/augur/33.0.1/)</li><li>[33.1.0](./build-files/augur/33.1.0/)</li><li>[33.2.0](./build-files/augur/33.2.0/)</li></ul> </details> | https://github.com/nextstrain/augur |
| [Augur](https://hub.docker.com/r/staphb/augur) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/augur)](https://hub.docker.com/r/staphb/augur) | <details><summary>Click to see all versions</summary> <ul><li>[6.3.0](./build-files/augur/6.3.0/)</li><li>[7.0.2](./build-files/augur/7.0.2/)</li><li>[8.0.0](./build-files/augur/8.0.0/)</li><li>[9.0.0](./build-files/augur/9.0.0/)</li><li>[16.0.3](./build-files/augur/16.0.3/)</li><li>[24.2.2](./build-files/augur/24.2.2/)</li><li>[24.2.3](./build-files/augur/24.2.3/)</li><li>[24.3.0](./build-files/augur/24.3.0/)</li><li>[24.4.0](./build-files/augur/24.4.0/)</li><li>[26.0.0](./build-files/augur/26.0.0/)</li><li>[27.0.0](./build-files/augur/27.0.0/)</li><li>[28.0.1](./build-files/augur/28.0.1/)</li><li>[29.0.0](./build-files/augur/29.0.0/)</li><li>[30.0.0](./build-files/augur/30.0.0/)</li><li>[31.1.0](./build-files/augur/31.1.0/)</li><li>[31.3.0](./build-files/augur/31.3.0/)</li><li>[31.4.0](./build-files/augur/31.4.0/)</li><li>[31.5.0](./build-files/augur/31.5.0/)</li><li>[32.0.0](./build-files/augur/32.0.0/)</li><li>[32.1.0](./build-files/augur/32.1.0/)</li><li>[33.0.0](./build-files/augur/33.0.0/)</li><li>[33.0.1](./build-files/augur/33.0.1/)</li><li>[33.1.0](./build-files/augur/33.1.0/)</li><li>[33.2.0](./build-files/augur/33.2.0/)</li><li>[33.4.1](./build-files/augur/33.4.1/)</li></ul> </details> | https://github.com/nextstrain/augur |
| [Auspice](https://hub.docker.com/r/staphb/auspice) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/auspice)](https://hub.docker.com/r/staphb/auspice) | <details><summary>Click to see all versions</summary> <ul><li>[2.12.0](./build-files/auspice/2.12.0/)</li><li>[2.68.0](./build-files/auspice/2.68.0/)</li></ul> </details> | https://github.com/nextstrain/auspice |
| [Autocycler](https://hub.docker.com/r/staphb/autocycler) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/autocycler)](https://hub.docker.com/r/staphb/autocycler) | <details><summary>Click to see all versions</summary> <ul><li>[0.2.1](./build-files/autocycler/0.2.1/)</li><li>[0.2.1-tutorial](./build-files/autocycler/0.2.1-tutorial/)</li><li>[0.4.0](./build-files/autocycler/0.4.0/)</li><li>[0.4.0-tutorial](./build-files/autocycler/0.4.0-tutorial/)</li><li>[0.6.1](./build-files/autocycler/0.6.1/)</li><li>[0.6.1-tutorial](./build-files/autocycler/0.6.1-tutorial/)</li>li>[0.6.2](./build-files/autocycler/0.6.2/)</li><li>[0.6.2-tutorial](./build-files/autocycler/0.6.2-tutorial/)</li></ul> </details> | https://github.com/rrwick/Autocycler/ |
| [bakta](https://hub.docker.com/r/staphb/bakta) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/bakta)](https://hub.docker.com/r/staphb/bakta) | <details><summary>Click to see all versions</summary> <ul><li>[1.9.2](./build-files/bakta/1.9.2/)</li><li>[1.9.2-light](./build-files/bakta/1.9.2-5.1-light/)</li><li>[1.9.3](./build-files/bakta/1.9.3/)</li><li>[1.9.3-light](./build-files/bakta/1.9.3-5.1-light/)</li><li>[1.9.4](./build-files/bakta/1.9.4/)</li><li>[1.9.4-5.1-light](./build-files/bakta/1.9.4-5.1-light/)</li><li>[1.10.3](./build-files/bakta/1.10.3/)</li><li>[1.10.3-light](./build-files/bakta/1.10.3-5.1-light/)</li><li>[1.10.4](./build-files/bakta/1.10.4/)</li><li>[1.10.4-5.1-light](./build-files/bakta/1.10.4-5.1-light/)</li><li>[1.11.0](./build-files/bakta/1.11.0/)</li><li>[1.11.0-6.0-light](./build-files/bakta/1.11.0-6.0-light/)</li><li>[1.11.3](./build-files/bakta/1.11.3/)</li><li>[1.11.3-6.0-light](./build-files/bakta/1.11.3-6.0-light/)</li><li>[1.11.4](./build-files/bakta/1.11.4/)</li><li>[1.11.4-6.0-light](./build-files/bakta/1.11.4-6.0-light/)</li><li>[1.12.0](./build-files/bakta/1.12.0/)</li><li>[1.12.0-6.0-light](./build-files/bakta/1.12.0-6.0-light/)</li></ul> </details> | https://github.com/oschwengers/bakta |
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121 changes: 121 additions & 0 deletions build-files/augur/33.4.1/Dockerfile
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FROM python:3.12-slim AS app

ARG AUGUR_VER="33.4.1"
ARG SEQKIT_VER="2.13.0"

# LABEL instructions tag the image with metadata that might be important to the user
# Optional, but highly recommended
LABEL base.image="python:3.12-slim"
LABEL dockerfile.version="1"
LABEL software="augur"
LABEL software.version=${AUGUR_VER}
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."
LABEL website="https://github.com/nextstrain/augur"
LABEL license="https://github.com/nextstrain/augur/blob/master/LICENSE.txt"
LABEL maintainer="John Arnn"
LABEL maintainer.email="jarnn@utah.gov"

# 'RUN' executes code during the build
# Install dependencies via apt-get or yum if using a centos or fedora base
RUN apt-get update && apt-get install -y --no-install-recommends \
procps \
ca-certificates \
wget \
mafft \
iqtree \
raxml \
fasttree \
vcftools && \
apt-get autoclean && rm -rf /var/lib/apt/lists/*

# install seqkit
RUN wget -q https://github.com/shenwei356/seqkit/releases/download/v${SEQKIT_VER}/seqkit_linux_amd64.tar.gz && \
tar -xzf seqkit_linux_amd64.tar.gz && \
mv seqkit /usr/local/bin/. && \
rm seqkit_linux_amd64.tar.gz

# install augur
RUN wget -q https://github.com/nextstrain/augur/archive/refs/tags/${AUGUR_VER}.tar.gz && \
tar -xzf ${AUGUR_VER}.tar.gz && \
pip install ${AUGUR_VER}.tar.gz --no-cache-dir && \
rm -v ${AUGUR_VER}.tar.gz

# augur tree calls iqtree
RUN ln -s /usr/bin/iqtree2 /usr/bin/iqtree

CMD [ "augur", "--help" ]

WORKDIR /data

FROM app AS test

RUN augur --help && augur version

WORKDIR /test

RUN apt-get update && apt-get install -y --no-install-recommends git

RUN git clone https://github.com/nextstrain/zika-tutorial && \
cd zika-tutorial && \
mkdir results && \
augur index \
--sequences data/sequences.fasta \
--output results/sequence_index.tsv && \
augur filter \
--sequences data/sequences.fasta \
--sequence-index results/sequence_index.tsv \
--metadata data/metadata.tsv \
--exclude config/dropped_strains.txt \
--output-sequences results/filtered.fasta \
--group-by country year month \
--sequences-per-group 20 \
--min-date 2012 && \
augur align \
--sequences results/filtered.fasta \
--reference-sequence config/zika_outgroup.gb \
--output results/aligned.fasta \
--fill-gaps && \
augur tree \
--alignment results/aligned.fasta \
--output results/tree_raw.nwk && \
augur refine \
--tree results/tree_raw.nwk \
--alignment results/aligned.fasta \
--metadata data/metadata.tsv \
--output-tree results/tree.nwk \
--output-node-data results/branch_lengths.json \
--timetree \
--coalescent opt \
--date-confidence \
--date-inference marginal \
--clock-filter-iqd 4 && \
augur traits \
--tree results/tree.nwk \
--metadata data/metadata.tsv \
--output-node-data results/traits.json \
--columns region country \
--confidence && \
augur ancestral \
--tree results/tree.nwk \
--alignment results/aligned.fasta \
--output-node-data results/nt_muts.json \
--inference joint && \
augur translate \
--tree results/tree.nwk \
--ancestral-sequences results/nt_muts.json \
--reference-sequence config/zika_outgroup.gb \
--output-node-data results/aa_muts.json && \
augur export v2 \
--tree results/tree.nwk \
--metadata data/metadata.tsv \
--node-data results/branch_lengths.json \
results/traits.json \
results/nt_muts.json \
results/aa_muts.json \
--colors config/colors.tsv \
--lat-longs config/lat_longs.tsv \
--auspice-config config/auspice_config.json \
--output auspice/zika.json && \
head auspice/zika.json

RUN pip list
90 changes: 90 additions & 0 deletions build-files/augur/33.4.1/README.md
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# Augur Container

Main tool: [Augur](https://github.com/nextstrain/augur)

Definition: One held to foretell events by omens.

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.

The output of augur is a series of JSONs that can be used to visualize your results using Auspice.

Note: Auspice is a different tool.

## Additional dependencies

- fasttree 2.1.11-2
- python 3.12.13
- iqtree 2.0.7+dfsg-1+b2
- mafft 7.505-1
- raxml 8.2.13+dfsg-2+b1
- vcftools 0.1.16-3+b1
- seqkit 2.13.0

<details>

<summary>Additional tools installed via pip:</summary>

```
Package Version
------------------------- -----------
attrs 26.1.0
backports.zstd 1.6.0
bcbio-gff 0.7.1
biopython 1.87
contourpy 1.3.3
cvxopt 1.3.3
cycler 0.12.1
docutils 0.23
fonttools 4.63.0
isal 1.8.0
isodate 0.7.2
jsonschema 4.26.0
jsonschema-specifications 2025.9.1
kiwisolver 1.5.0
matplotlib 3.11.0
networkx 3.6.1
nextstrain-augur 33.4.1
numpy 2.5.0
packaging 26.2
pandas 2.3.3
phylo-treetime 0.12.1
pillow 12.2.0
pip 25.0.1
pyfastx 2.3.1
pyparsing 3.3.2
python-calamine 0.7.0
python-dateutil 2.9.0.post0
pytz 2026.2
PyYAML 6.0.3
referencing 0.37.0
rpds-py 2026.5.1
scipy 1.18.0
six 1.17.0
typing_extensions 4.15.0
tzdata 2026.2
xopen 2.1.0
zlib-ng 1.0.0

```

</details>

## Example Usage

```bash
augur index --sequences sequences.fasta --output sequence_index.tsv
```

```bash
augur filter \
--sequences data/sequences.fasta \
--sequence-index results/sequence_index.tsv \
--metadata data/metadata.tsv \
--exclude config/dropped_strains.txt \
--output-sequences results/filtered.fasta \
--group-by country year month \
--sequences-per-group 20 \
--min-date 2012
```

Better documentation can be found [here.](https://docs.nextstrain.org/en/latest/tutorials/creating-a-workflow.html)
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