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updating augur to version 26.0.0 (#1054)
* updating augur to version 26.0.0 * minor changes to dockerfile to silence warnings, quiet down some output, and use recommend CMD format --------- Co-authored-by: Curtis Kapsak <[email protected]>
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| FROM python:3.11-slim AS app | ||
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| ARG AUGUR_VER="26.0.0" | ||
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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=${AUGUR_VER} | ||
| LABEL description="Augur is the bioinformatics toolkit we use to track evolution from sequence and serological data.The output of augur is a series of JSONs that can be used to visualize your results using Auspice." | ||
| LABEL website="https://github.com/nextstrain/augur" | ||
| LABEL license="https://github.com/nextstrain/augur/blob/master/LICENSE.txt" | ||
| LABEL maintainer="John Arnn" | ||
| LABEL maintainer.email="[email protected]" | ||
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| # 'RUN' executes code during the build | ||
| # Install dependencies via apt-get or yum if using a centos or fedora base | ||
| RUN apt-get update && apt-get install -y --no-install-recommends \ | ||
| procps \ | ||
| ca-certificates \ | ||
| wget \ | ||
| mafft \ | ||
| iqtree \ | ||
| raxml \ | ||
| fasttree \ | ||
| vcftools && \ | ||
| apt-get autoclean && rm -rf /var/lib/apt/lists/* | ||
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| RUN wget -q https://github.com/nextstrain/augur/archive/refs/tags/${AUGUR_VER}.tar.gz && \ | ||
| tar -xzf ${AUGUR_VER}.tar.gz && \ | ||
| pip install ${AUGUR_VER}.tar.gz && \ | ||
| rm -v ${AUGUR_VER}.tar.gz | ||
| #&& \ | ||
| #cd augur-${AUGUR_VER} && \ | ||
| #python3 -m pip install '.[full]' | ||
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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 \ | ||
| --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 |
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| # Augur Container | ||
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| Main tool: [Augur](https://github.com/nextstrain/augur) | ||
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| Additional tools: | ||
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| - mafft 7.505 | ||
| - iqtree2 2.0.7 | ||
| - raxml 8.2.12 | ||
| - fasttree 2.1.11 | ||
| - vcftools 0.1.16 | ||
| - biopython 1.84 | ||
| - matplotlib 3.9.2 | ||
| - numpy 1.26.4 | ||
| - pandas 1.5.3 | ||
| - phylo-treetime 0.11.4 | ||
| - python 3.11.10 | ||
| - scipy 1.14.1 | ||
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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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| ## 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) |