FROM python:3.6.4-slim-stretch

RUN groupadd user && \
    useradd --create-home --home-dir /home/user -g user -s /bin/bash user

WORKDIR /home/user

# install sra-toolkit 2.8.2-1 and requirements

ADD Pipfile Pipfile.lock ./

RUN apt-get update && \
    apt-get install -y git libgomp1 build-essential libssl-dev libcurl4-openssl-dev curl && \
    curl --output sratoolkit.tar.gz https://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/2.8.2-1/sratoolkit.2.8.2-1-ubuntu64.tar.gz && \
    tar xf sratoolkit.tar.gz && \
    rm sratoolkit.tar.gz && \
    find sratoolkit.2.8.2-1-ubuntu64 ! -type d ! -name "fastq-dump*" -a ! -name "*.kfg" -delete && \
    pip install pipenv && \
    pipenv install --system --deploy && \
    pip install "git+https://github.com/dib-lab/sourmash.git@master" && \
    apt-get remove -y curl git build-essential libssl-dev && \
    apt-get autoremove -y

ENV PATH $PATH:/home/user/sratoolkit.2.8.2-1-ubuntu64/bin/

USER user

# Configure sra-toolkit to disable cache
RUN mkdir .ncbi
RUN echo '/repository/user/cache-disabled = "true"' > .ncbi/user-settings.mkfg

COPY wort wort
COPY config config

CMD celery -A wort.blueprints.compute.tasks --without-gossip --without-mingle --without-heartbeat -l INFO -c 1 worker