Dockerfile

FROM ubuntu:bionic

LABEL base.image="ubuntu:bionic"
LABEL dockerfile.version="2"
LABEL software="ARIBA"
LABEL software.version="2.14.4"
LABEL description="ARIBA: Antimicrobial Resistance Identification By Assembly"
LABEL website="https://github.com/sanger-pathogens/ariba"
LABEL license="https://github.com/sanger-pathogens/ariba/blob/master/LICENSE"
LABEL maintainer="Curtis Kapsak"
LABEL maintainer.email="pjx8@cdc.gov"

# prevents having to enter commands during apt-get install
ENV DEBIAN_FRONTEND=noninteractive

# py2=2.7.17
# py3=3.6.9
# cd-hit=4.7
# mummer=3.23
# bowtie2=2.3.4.1
RUN apt-get update && apt-get install --no-install-recommends -y \
 python3-dev \
 python3-pip \
 python3-tk \
 python3-setuptools \
 python3-wheel \
 cython3 \
 zlib1g-dev \
 bowtie2 \
 mummer \
 cd-hit \
 wget \
 curl \
 gawk \
 locales-all \
 build-essential \
 libbz2-dev \
 liblzma-dev  \
 autoconf \
 automake \
 perl \
 libcurl4-gnutls-dev \
 libssl-dev && \
 rm -rf /var/lib/apt/lists/*

ENV LANG=en_US.UTF-8 \
    LANGUAGE=en_US:en 

# SPAdes 3.13.1 (listed in their dockerfile, but not on README...)
RUN wget http://cab.spbu.ru/files/release3.13.1/SPAdes-3.13.1-Linux.tar.gz && \
  tar -xzf SPAdes-3.13.1-Linux.tar.gz && \
  rm -r SPAdes-3.13.1-Linux.tar.gz && \
  mkdir /data

# needed to avoid a matplotlib error
# https://github.com/sanger-pathogens/ariba/blob/b51b524c9d9588cba9d998c9121bd74c63856526/Dockerfile#L49
ENV MPLBACKEND="agg"

# ARIBA=2.14.4
# This installs: BeautifulSoup4-4.9.0 ariba-2.14.4 biopython-1.76 cycler-0.10.0 dendropy-4.4.0 
# kiwisolver-1.2.0 matplotlib-3.2.1 numpy-1.18.4 pyfastaq-3.17.0 pymummer-0.10.3 pyparsing-2.4.7 
# pysam-0.15.4 python-dateutil-2.8.1 six-1.14.0 soupsieve-2.0
# pysam=0.16.0 breaks ariba 2.14.4 (June 2020)
RUN pip3 install pysam==0.15.4 ariba==2.14.4

# set $PATH and locale settings for singularity compatibility
ENV PATH="$PATH:/SPAdes-3.13.1-Linux/bin" \
 LC_ALL=C

WORKDIR /data