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| 1 | +FROM python:3.12-slim AS app |
| 2 | + |
| 3 | +ARG AUGUR_VER="33.4.1" |
| 4 | +ARG SEQKIT_VER="2.13.0" |
| 5 | + |
| 6 | +# LABEL instructions tag the image with metadata that might be important to the user |
| 7 | +# Optional, but highly recommended |
| 8 | +LABEL base.image="python:3.12-slim" |
| 9 | +LABEL dockerfile.version="1" |
| 10 | +LABEL software="augur" |
| 11 | +LABEL software.version=${AUGUR_VER} |
| 12 | +LABEL description="Augur is the bioinformatics toolkit we use to track evolution from sequence and serological data.The output of augur is a series of JSONs that can be used to visualize your results using Auspice." |
| 13 | +LABEL website="https://github.com/nextstrain/augur" |
| 14 | +LABEL license="https://github.com/nextstrain/augur/blob/master/LICENSE.txt" |
| 15 | +LABEL maintainer="John Arnn" |
| 16 | +LABEL maintainer.email="jarnn@utah.gov" |
| 17 | + |
| 18 | +# 'RUN' executes code during the build |
| 19 | +# Install dependencies via apt-get or yum if using a centos or fedora base |
| 20 | +RUN apt-get update && apt-get install -y --no-install-recommends \ |
| 21 | + procps \ |
| 22 | + ca-certificates \ |
| 23 | + wget \ |
| 24 | + mafft \ |
| 25 | + iqtree \ |
| 26 | + raxml \ |
| 27 | + fasttree \ |
| 28 | + vcftools && \ |
| 29 | + apt-get autoclean && rm -rf /var/lib/apt/lists/* |
| 30 | + |
| 31 | +# install seqkit |
| 32 | +RUN wget -q https://github.com/shenwei356/seqkit/releases/download/v${SEQKIT_VER}/seqkit_linux_amd64.tar.gz && \ |
| 33 | + tar -xzf seqkit_linux_amd64.tar.gz && \ |
| 34 | + mv seqkit /usr/local/bin/. && \ |
| 35 | + rm seqkit_linux_amd64.tar.gz |
| 36 | + |
| 37 | +# install augur |
| 38 | +RUN wget -q https://github.com/nextstrain/augur/archive/refs/tags/${AUGUR_VER}.tar.gz && \ |
| 39 | + tar -xzf ${AUGUR_VER}.tar.gz && \ |
| 40 | + pip install ${AUGUR_VER}.tar.gz --no-cache-dir && \ |
| 41 | + rm -v ${AUGUR_VER}.tar.gz |
| 42 | + |
| 43 | +# augur tree calls iqtree |
| 44 | +RUN ln -s /usr/bin/iqtree2 /usr/bin/iqtree |
| 45 | + |
| 46 | +CMD [ "augur", "--help" ] |
| 47 | + |
| 48 | +WORKDIR /data |
| 49 | + |
| 50 | +FROM app AS test |
| 51 | + |
| 52 | +RUN augur --help && augur version |
| 53 | + |
| 54 | +WORKDIR /test |
| 55 | + |
| 56 | +RUN apt-get update && apt-get install -y --no-install-recommends git |
| 57 | + |
| 58 | +RUN git clone https://github.com/nextstrain/zika-tutorial && \ |
| 59 | + cd zika-tutorial && \ |
| 60 | + mkdir results && \ |
| 61 | + augur index \ |
| 62 | + --sequences data/sequences.fasta \ |
| 63 | + --output results/sequence_index.tsv && \ |
| 64 | + augur filter \ |
| 65 | + --sequences data/sequences.fasta \ |
| 66 | + --sequence-index results/sequence_index.tsv \ |
| 67 | + --metadata data/metadata.tsv \ |
| 68 | + --exclude config/dropped_strains.txt \ |
| 69 | + --output-sequences results/filtered.fasta \ |
| 70 | + --group-by country year month \ |
| 71 | + --sequences-per-group 20 \ |
| 72 | + --min-date 2012 && \ |
| 73 | + augur align \ |
| 74 | + --sequences results/filtered.fasta \ |
| 75 | + --reference-sequence config/zika_outgroup.gb \ |
| 76 | + --output results/aligned.fasta \ |
| 77 | + --fill-gaps && \ |
| 78 | + augur tree \ |
| 79 | + --alignment results/aligned.fasta \ |
| 80 | + --output results/tree_raw.nwk && \ |
| 81 | + augur refine \ |
| 82 | + --tree results/tree_raw.nwk \ |
| 83 | + --alignment results/aligned.fasta \ |
| 84 | + --metadata data/metadata.tsv \ |
| 85 | + --output-tree results/tree.nwk \ |
| 86 | + --output-node-data results/branch_lengths.json \ |
| 87 | + --timetree \ |
| 88 | + --coalescent opt \ |
| 89 | + --date-confidence \ |
| 90 | + --date-inference marginal \ |
| 91 | + --clock-filter-iqd 4 && \ |
| 92 | + augur traits \ |
| 93 | + --tree results/tree.nwk \ |
| 94 | + --metadata data/metadata.tsv \ |
| 95 | + --output-node-data results/traits.json \ |
| 96 | + --columns region country \ |
| 97 | + --confidence && \ |
| 98 | + augur ancestral \ |
| 99 | + --tree results/tree.nwk \ |
| 100 | + --alignment results/aligned.fasta \ |
| 101 | + --output-node-data results/nt_muts.json \ |
| 102 | + --inference joint && \ |
| 103 | + augur translate \ |
| 104 | + --tree results/tree.nwk \ |
| 105 | + --ancestral-sequences results/nt_muts.json \ |
| 106 | + --reference-sequence config/zika_outgroup.gb \ |
| 107 | + --output-node-data results/aa_muts.json && \ |
| 108 | + augur export v2 \ |
| 109 | + --tree results/tree.nwk \ |
| 110 | + --metadata data/metadata.tsv \ |
| 111 | + --node-data results/branch_lengths.json \ |
| 112 | + results/traits.json \ |
| 113 | + results/nt_muts.json \ |
| 114 | + results/aa_muts.json \ |
| 115 | + --colors config/colors.tsv \ |
| 116 | + --lat-longs config/lat_longs.tsv \ |
| 117 | + --auspice-config config/auspice_config.json \ |
| 118 | + --output auspice/zika.json && \ |
| 119 | + head auspice/zika.json |
| 120 | + |
| 121 | +RUN pip list |
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