Dockerfile

FROM python:3.11-slim AS app

ARG AUGUR_VER="27.0.0"

# 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"

# '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/*

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 

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

WORKDIR /data

FROM app AS test

RUN augur --help

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 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