Dockerfile

# Base Image
FROM ubuntu:xenial

# Metadata
LABEL base.image="ubuntu:xenial"
LABEL version="1"
LABEL software="SeqSero2"
LABEL software.version="1.1.0"
LABEL description="Salmonella serotyping from genome sequencing data"
LABEL website="https://github.com/denglab/SeqSero2"
LABEL license="https://github.com/denglab/SeqSero2/blob/master/LICENSE"
LABEL maintainer1="Jake Garfin"
LABEL maintainer1.email="jake.garfin@state.mn.us"
LABEL maintainer2="Curtis Kapsak"
LABEL maintainer2.email="pjx8@cdc.gov"
LABEL maintainer3="Kelsey Florek"
LABEL maintainer3.email="kelsey.florek@slh.wisc.edu"

RUN apt-get update && apt-get install -y \
  python3\
  python3-pip\
  bwa\
  ncbi-blast+\
  sra-toolkit\
  bedtools\
  wget\
  zlib1g-dev\
  libbz2-dev\
  liblzma-dev\
  build-essential\
  libncurses5-dev

# Install samtools (installing from apt breaks SeqSero2 version check)
RUN wget 'https://github.com/samtools/samtools/releases/download/1.9/samtools-1.9.tar.bz2' && \
  tar -xvf samtools-1.9.tar.bz2 && rm samtools-1.9.tar.bz2 && cd samtools-1.9 && make

# Install salmID 0.122
RUN wget https://github.com/hcdenbakker/SalmID/archive/0.122.tar.gz && \
  tar -xzf 0.122.tar.gz && rm -rf 0.122.tar.gz

# Install SPAdes 3.9.0
RUN wget https://github.com/ablab/spades/releases/download/v3.9.0/SPAdes-3.9.0-Linux.tar.gz && \
  tar -xzf SPAdes-3.9.0-Linux.tar.gz && \
  rm -rf SPAdes-3.9.0-Linux.tar.gz

# Install SeqSero2 1.0.2
RUN wget https://github.com/denglab/SeqSero2/archive/v1.1.0.tar.gz && \
  tar -xzf v1.1.0.tar.gz && \
  rm -rf v1.1.0.tar.gz && \
  cd /SeqSero2-1.1.0/ && \
  python3 -m pip install . && \
  mkdir /data

# PATH edited to include /SeqSero2-1.1.0/bin in previous python3 command
ENV PATH="${PATH}:/SPAdes-3.9.0-Linux/bin:/SalmID-0.122:/samtools-1.9" \
    LC_ALL=C

WORKDIR /data