docker-builds/build-files/staramr/0.11.1/Dockerfile at master · theiagen/docker-builds · GitHub

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# base image
FROM python:3.9-slim AS app

ARG STARAMR_VER="0.11.1"
ARG MLST_VER="2.23.0"
ARG ANY2FASTA_VERSION="0.4.2"

LABEL base.image="python:3.9-slim"
LABEL dockerfile.version="1"
LABEL software="staramr"
LABEL software.version="${STARAMR_VER}"
LABEL description="staramr scans bacterial genome contigs for AMR genes and plasmids"
LABEL website="https://github.com/phac-nml/staramr"
LABEL license="https://github.com/phac-nml/staramr/blob/master/LICENSE"
LABEL maintainer="Rachael St. Jacques"
LABEL maintainer.email="rachael.stjacques@dgs.virginia.gov"
LABEL maintainer2="Curtis Kapsak"
LABEL maintainer2.email="curtis.kapsak@theiagen.com"

# install dependencies via apt; cleanup apt garbage
# ncbi-blast+ is v2.9.0 in ubuntu:focal (as of August 2022)
RUN apt-get update && apt-get install -y --no-install-recommends \
  git \
  wget \
  libmoo-perl \
  liblist-moreutils-perl \
  libjson-perl \
  gzip \
  file \
  ncbi-blast+ \
  procps \
  ca-certificates && \
  apt-get autoclean && rm -rf /var/lib/apt/lists/*

# any2fasta
RUN wget -q https://github.com/tseemann/any2fasta/archive/refs/tags/v${ANY2FASTA_VERSION}.tar.gz && \
    tar -xvf v${ANY2FASTA_VERSION}.tar.gz && \
    rm v${ANY2FASTA_VERSION}.tar.gz && \
    cd any2fasta-${ANY2FASTA_VERSION} && \
    chmod +x any2fasta

# mlst
# apt dependencies: wget libmoo-perl liblist-moreutils-perl libjson-perl gzip file
# also requires blast 2.9.0 or greater
RUN wget -q https://github.com/tseemann/mlst/archive/v${MLST_VER}.tar.gz && \
  tar -xzf v${MLST_VER}.tar.gz && \
  rm v${MLST_VER}.tar.gz

# staramr; make /data
RUN wget -q https://github.com/phac-nml/staramr/archive/refs/tags/${STARAMR_VER}.tar.gz && \
  pip install ${STARAMR_VER}.tar.gz --no-cache-dir && \
  rm -rf ${STARAMR_VER}.tar.gz && \
  mkdir /data

# set $PATH and locale settings for singularity
ENV PATH="${PATH}:/mlst-${MLST_VER}/bin:/any2fasta-${ANY2FASTA_VERSION}/" \
    LC_ALL=C

# update staramr default databases and print db info
RUN staramr db update -d && staramr db info

CMD ["staramr", "--help"]

WORKDIR /data

FROM app AS test

RUN staramr --help && staramr --version

# download the FASTA file for ${GENBANK_ACCESSION}
# Salmonella Enterica isolate from PHE-UK: https://www.ncbi.nlm.nih.gov/assembly/GCA_010941835.1/
RUN wget -q https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/010/941/835/GCA_010941835.1_PDT000052640.3/GCA_010941835.1_PDT000052640.3_genomic.fna.gz  && \
  gzip -d GCA_010941835.1_PDT000052640.3_genomic.fna.gz

# run staramr on the second genome mentioned on staramr's documentation; print resulting TSVs
RUN staramr search -o /data/staramr-test-Salmonella \
  --pointfinder-organism salmonella \
  --plasmidfinder-database-type enterobacteriales \
  /data/GCA_010941835.1_PDT000052640.3_genomic.fna

# installing bsdmainutils for installing "column" command
RUN apt-get update && apt-get install -y --no-install-recommends bsdmainutils

# neatly print out resulting/output TSVs
RUN column -t /data/staramr-test-Salmonella/mlst.tsv && echo && \
  column -t /data/staramr-test-Salmonella/pointfinder.tsv && echo && \
  column -t /data/staramr-test-Salmonella/plasmidfinder.tsv && echo && \
  column -t /data/staramr-test-Salmonella/resfinder.tsv && echo && \
  column -t /data/staramr-test-Salmonella/detailed_summary.tsv && echo && \
  column -t /data/staramr-test-Salmonella/summary.tsv

RUN staramr db info