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FROM ubuntu:17.10
RUN apt-get update
RUN apt-get install --no-install-recommends -y \
build-essential \
cd-hit \
curl \
git \
libbz2-dev \
liblzma-dev \
mummer \
python \
python3-dev \
python3-setuptools \
python3-pip \
python3-tk \
python3-matplotlib \
unzip \
wget \
zlib1g-dev
RUN wget -q http://downloads.sourceforge.net/project/bowtie-bio/bowtie2/2.2.9/bowtie2-2.2.9-linux-x86_64.zip \
&& unzip bowtie2-2.2.9-linux-x86_64.zip \
&& rm bowtie2-2.2.9-linux-x86_64.zip
# Need MPLBACKEND="agg" to make matplotlib work without X11, otherwise get the error
# _tkinter.TclError: no display name and no $DISPLAY environment variable
ENV ARIBA_BOWTIE2=$PWD/bowtie2-2.2.9/bowtie2 ARIBA_CDHIT=cdhit-est MPLBACKEND="agg"
RUN git clone https://github.com/sanger-pathogens/ariba.git \
&& cd ariba \
&& git checkout v2.12.0 \
&& python3 setup.py test \
&& python3 setup.py install
CMD ariba
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