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Dockerfile
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FROM ubuntu:jammy as app
ARG PANGO_ALIASOR_VER="0.3.0"
LABEL base.image="ubuntu:jammy"
LABEL dockerfile.version="1"
LABEL software="Pango Aliasor"
LABEL software.version="${PANGO_ALIASOR_VER}"
LABEL description="Links sublineages to parent pangolin lineages"
LABEL website="https://github.com/corneliusroemer/pango_aliasor"
LABEL license="https://github.com/corneliusroemer/pango_aliasor/blob/main/LICENSE"
LABEL maintainer="Erin Young"
LABEL maintainer.email="[email protected]"
RUN apt-get update && apt-get install -y --no-install-recommends \
python3 \
python3-pip \
python-is-python3 \
wget \
procps && \
apt-get autoclean && rm -rf /var/lib/apt/lists/*
RUN wget -q https://github.com/corneliusroemer/pango_aliasor/archive/refs/tags/v${PANGO_ALIASOR_VER}.tar.gz && \
pip install v${PANGO_ALIASOR_VER}.tar.gz && \
rm v${PANGO_ALIASOR_VER}.tar.gz && \
pip install --no-cache pandas && \
mkdir /data
ENV PATH="$PATH" LC_ALL=C
COPY aliasor.py /usr/bin/.
WORKDIR /key
RUN wget -q https://raw.githubusercontent.com/cov-lineages/pango-designation/master/pango_designation/alias_key.json
WORKDIR /data
CMD [ "aliasor.py", "--help" ]
FROM staphb/pangolin:4.3.1-pdata-1.28 as pangolin
RUN apt-get update && apt-get install -y --no-install-recommends zstd
RUN wget -q https://github.com/corneliusroemer/pango-sequences/raw/main/data/pango-consensus-sequences_genome-nuc.fasta.zst && \
zstd -d pango-consensus-sequences_genome-nuc.fasta.zst && \
pangolin pango-consensus-sequences_genome-nuc.fasta
FROM app as test
WORKDIR /test
RUN aliasor.py --help
COPY --from=pangolin /data/lineage_report.csv .
RUN aliasor.py --input lineage_report.csv --output aliased_lineage_report_github.tsv && \
aliasor.py --input lineage_report.csv --output aliased_lineage_report.tsv --alias-key /key/alias_key.json && \
wc -l aliased_lineage_report_github.tsv aliased_lineage_report.tsv && \
head aliased_lineage_report_github.tsv aliased_lineage_report.tsv