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Dockerfile
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FROM python:3.7.1-stretch
MAINTAINER Joel Nitta <joelnitta@gmail.com>
ENV DEBIAN_FRONTEND noninteractive
RUN apt-get update && apt-get install -y \
time \
bwa \
exonerate \
ncbi-blast+ \
parallel \
samtools \
&& apt-get clean && apt-get purge \
&& pip3 install biopython \
&& mkdir /apps
# Silence parallel citation warning
RUN mkdir /root/.parallel \
&& touch /root/.parallel/will-cite
WORKDIR /apps
# SPAdes is available as a debian package, but doesn't work for HybPiper.
# Use linux binary instead.
RUN wget http://cab.spbu.ru/files/release3.13.0/SPAdes-3.13.0-Linux.tar.gz \
&& tar xf SPAdes-3.13.0-Linux.tar.gz \
&& rm SPAdes-3.13.0-Linux.tar.gz
ENV PATH="$PATH:/apps/SPAdes-3.13.0-Linux/bin/"
# Clone hybpiper and checkout most recent commit at time of building docker image
RUN git clone https://github.com/joelnitta/HybPiper.git \
&& cd HybPiper \
&& git checkout 58907ae6366f7fdbdf548486adee120d6e54ed21 \
&& chmod +x *.py
ENV PATH="$PATH:/apps/HybPiper/"
WORKDIR /home
ENTRYPOINT /bin/bash