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adding augur version 32.1.0 #1518
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| FROM python:3.11-slim AS app | ||
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| ARG AUGUR_VER="32.1.0" | ||
| ARG SEQKIT_VER="2.12.0" | ||
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| # LABEL instructions tag the image with metadata that might be important to the user | ||
| # Optional, but highly recommended | ||
| LABEL base.image="python:3.11-slim" | ||
| LABEL dockerfile.version="1" | ||
| LABEL software="augur" | ||
| LABEL software.version=${AUGUR_VER} | ||
| LABEL description="Augur is the bioinformatics toolkit we use to track evolution from sequence and serological data.The output of augur is a series of JSONs that can be used to visualize your results using Auspice." | ||
| LABEL website="https://github.com/nextstrain/augur" | ||
| LABEL license="https://github.com/nextstrain/augur/blob/master/LICENSE.txt" | ||
| LABEL maintainer="John Arnn" | ||
| LABEL maintainer.email="jarnn@utah.gov" | ||
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| # 'RUN' executes code during the build | ||
| # Install dependencies via apt-get or yum if using a centos or fedora base | ||
| RUN apt-get update && apt-get install -y --no-install-recommends \ | ||
| procps \ | ||
| ca-certificates \ | ||
| wget \ | ||
| mafft \ | ||
| iqtree \ | ||
| raxml \ | ||
| fasttree \ | ||
| vcftools && \ | ||
| apt-get autoclean && rm -rf /var/lib/apt/lists/* | ||
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| # install seqkit | ||
| RUN wget -q https://github.com/shenwei356/seqkit/releases/download/v${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 | ||
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| # 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 | ||
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| # augur tree calls iqtree | ||
| 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 && \ | ||
| 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 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 | ||
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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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| - biopython 1.85 | ||
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| - fasttree 2.1.11 | ||
| - python 3.11.13 | ||
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| - iqtree2 2.0.7 | ||
| - mafft 7.505 | ||
| - matplotlib 3.10.6 | ||
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| - numpy 2.3.3 | ||
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| - pandas 2.3.3 | ||
| - raxml 8.2.12 | ||
| - scipy 1.16.2 | ||
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| - vcftools 0.1.16 | ||
| - seqkit 2.12.0 | ||
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| ## Example Usage | ||
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| ```bash | ||
| augur index --sequences sequences.fasta --output sequence_index.tsv | ||
| ``` | ||
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| ```bash | ||
| augur filter \ | ||
| --sequences data/sequences.fasta \ | ||
| --sequence-index results/sequence_index.tsv \ | ||
| --metadata data/metadata.tsv \ | ||
| --exclude config/dropped_strains.txt \ | ||
| --output results/filtered.fasta \ | ||
| --group-by country year month \ | ||
| --sequences-per-group 20 \ | ||
| --min-date 2012 | ||
| ``` | ||
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| Better documentation can be found [here.](https://docs.nextstrain.org/en/latest/tutorials/creating-a-workflow.html) | ||
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should be changed to
--output-sequences results/filtered.fastaas--outputis deprecated and will be removed in the next major releaseThere was a problem hiding this comment.
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Is this only the case with augur filter? Or are there others that need to be updated too?
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I think so, yes. I was going off of warnings in the the original github actions workflow and they have disappeared after your latest commit. Thanks for changing that!