Dockerfile

# golob/arf:0.1

FROM      ubuntu:18.04

ENV DEBIAN_FRONTEND=noninteractive
RUN apt-get update && apt-get install -y \
python3-dev \
python3-pip \
postgresql \
wget \
git \
&& apt-get clean \
&& apt-get purge \
&& rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*

RUN pip3 install pip --upgrade

RUN pip3 install \
        awscli \
        boto3 \
        numpy \
        biopython==1.77 \
        Cython \
        taxtastic

RUN mkdir -p /src

RUN mkdir /logs && mkdir /records

RUN cd /src && \
wget https://github.com/torognes/vsearch/releases/download/v2.15.1/vsearch-2.15.1-linux-x86_64.tar.gz && \
tar xzvf vsearch-2.15.1-linux-x86_64.tar.gz && \
cp /src/vsearch-2.15.1-linux-x86_64/bin/vsearch /usr/local/bin/ && \
rm -r /src/*

RUN cd /src && \
wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.11.0/ncbi-blast-2.11.0+-x64-linux.tar.gz && \
tar xzvf ncbi-blast-2.11.0+-x64-linux.tar.gz && \
cp  /src/ncbi-blast-2.11.0+/bin/makeblastdb /usr/local/bin && \
rm -r /src/*

ADD requirements.txt /src/
RUN pip3 install -r /src/requirements.txt && rm -r /src/*

RUN mkdir -p /db/
ADD data/rdp_16s_type_strains.fasta.bz2 /db/
RUN cd /db/ && bunzip2 rdp_16s_type_strains.fasta.bz2 -c > gzip > rdp_16s_type_strains.fasta.gz

ADD bin/* /usr/local/bin/
RUN chmod +x /usr/local/bin/



WORKDIR /working